From yrzsma at rit.edu Mon May 1 11:28:38 2023 From: yrzsma at rit.edu (Yosef Zlochower) Date: Mon, 1 May 2023 16:28:38 +0000 Subject: [Users] 2023 North American Einstein Toolkit School and Workshop (hybrid) Message-ID: <3f78f7bb-bb94-5f7c-2666-e91f9b60ea9a@rit.edu> The 2023 North American Einstein Toolkit School and Workshop will be held at the Rochester Institute of Technology on July 17 through July 21. This will be a hybrid conference with talks and participants both in-person and over zoom. The Einstein Toolkit is a community-driven software platform of core computational tools to advance and support research in relativistic astrophysics and gravitational physics. The conference consist of a mixture of tutorials for new users and talks about the latest developments both in the toolkit and the larger scientific community. A preliminary schedule and links to the registration page can be found at https://compact-binaries.org/content/events/2023-07-17/north-american-einstein-toolkit-school-and-workshop Registration is now open and remain open until June 17, 2023. As part of the registration process, potential attendees can apply for partial travel support. In order to be eligible, applications must be received prior to June 1. Notification of partial travel support will be made by June 8. From shamims at iiserb.ac.in Wed May 3 04:41:49 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Wed, 3 May 2023 15:11:49 +0530 Subject: [Users] Compilation Error in cluster ParamGanga Message-ID: Dear all, We are trying to compile ETK on ParamGanga at IIT Roorkee. The compilation stops at a very initial step and gives out the error: *checking whether the Fortran compiler (gfortran ) works... yeschecking whether the Fortran compiler (gfortran ) is a cross-compiler... nochecking whether the Fortran compiler (gfortran ) supports TYPE(*) for CCTK_PointerTo... yeschecking how to run the C preprocessor... cppchecking for ANSI C header files... nochecking for C99 features... yeschecking for M_PI... noconfigure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.* We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. This error is consistent if we set up using Intel Compiler (2020 or 2019), or gcc (11 or 10). I have attached the outfile, error file, machine script, and option lists for both cases (Intel and gcc) for any reference. Secondly, we are not allowed to compile ETK on login nodes. So we are queuing a job script, which upon execution, enters the Cactus directory, does "setup-silent", and then executes the build command. Is this the right way to compile ETK using the batch script? Or should we do something different? I have attached the shell script (compile.sh) used for sbatch queue for reference. Thanks in advance for the help. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: paramganga.cfg Type: application/octet-stream Size: 2882 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: paramganga_gcc.ini Type: application/octet-stream Size: 3487 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: compile.out Type: application/octet-stream Size: 92720 bytes Desc: not available URL: From frank.loeffler at uni-jena.de Wed May 3 05:19:27 2023 From: frank.loeffler at uni-jena.de (Frank Loeffler) Date: Wed, 3 May 2023 12:19:27 +0200 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: Message-ID: Hi Shamim On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: >We are trying to compile ETK on ParamGanga at IIT Roorkee. The >compilation >stops at a very initial step and gives out the error: > >*checking whether the Fortran compiler (gfortran ) works... yeschecking >whether the Fortran compiler (gfortran ) is a cross-compiler... nochecking >whether the Fortran compiler (gfortran ) supports TYPE(*) for >CCTK_PointerTo... yeschecking how to run the C preprocessor... cppchecking >for ANSI C header files... nochecking for C99 features... yeschecking for >M_PI... noconfigure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to >CPPFLAGS.* > >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. This >error is consistent if we set up using Intel Compiler (2020 or 2019), or >gcc (11 or 10). I have attached the outfile, error file, machine script, >and option lists for both cases (Intel and gcc) for any reference. > >Secondly, we are not allowed to compile ETK on login nodes. So we are >queuing a job script, which upon execution, enters the Cactus directory, >does "setup-silent", and then executes the build command. Is this the right >way to compile ETK using the batch script? Or should we do something >different? I have attached the shell script (compile.sh) used for sbatch >queue for reference. I might be wrong, but setup-silent will not use your machine file which contains all the compiler flags, but will setup something "from scratch" instead. According to the logs, this will be, e.g., in /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini My guess would be that this misses the compiler flags necessary to have M_PI defined. The best way to get this working might be to let simfactory also detect the cluster configuration on the compute nodes (where you compile), such that setup-silent is not needed, but instead the correct cluster configuration is found and used automatically. In order to do that, look at examples of 'aliaspattern' in the mdb/machines directory. An alternative would be to tell simfactory specifically that you want to use your machine configuration file. As a side-note: I noticed the command 'patch' is missing too. This is a tool so common that it should be installed everywhere. Your admin is probably the best person to ask for advise here. It should not be too hard to install yourself, but that should not be necessary either, especially when you are told to compile on compute nodes. Frank -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: not available URL: From shamims at iiserb.ac.in Wed May 3 08:20:30 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Wed, 3 May 2023 18:50:30 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: Message-ID: Dear Frank, I added the alias pattern for the computing nodes and now ETK can detect the cluster (checked by asking "whoami") during the batch queuing. I'll get in touch with the admins to include 'patch'. However, the problem still persists, having assured that the correct machine file and option list are being used during the compilation. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Wed, May 3, 2023 at 3:49?PM Frank Loeffler wrote: > Hi Shamim > > On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: > >We are trying to compile ETK on ParamGanga at IIT Roorkee. The > >compilation > >stops at a very initial step and gives out the error: > > > >*checking whether the Fortran compiler (gfortran ) works... yeschecking > >whether the Fortran compiler (gfortran ) is a cross-compiler... > nochecking > >whether the Fortran compiler (gfortran ) supports TYPE(*) for > >CCTK_PointerTo... yeschecking how to run the C preprocessor... cppchecking > >for ANSI C header files... nochecking for C99 features... yeschecking for > >M_PI... noconfigure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE > to > >CPPFLAGS.* > > > >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. This > >error is consistent if we set up using Intel Compiler (2020 or 2019), or > >gcc (11 or 10). I have attached the outfile, error file, machine script, > >and option lists for both cases (Intel and gcc) for any reference. > > > >Secondly, we are not allowed to compile ETK on login nodes. So we are > >queuing a job script, which upon execution, enters the Cactus directory, > >does "setup-silent", and then executes the build command. Is this the > right > >way to compile ETK using the batch script? Or should we do something > >different? I have attached the shell script (compile.sh) used for sbatch > >queue for reference. > > I might be wrong, but setup-silent will not use your machine file which > contains all the compiler flags, but will setup something "from scratch" > instead. According to the logs, this will be, e.g., in > > > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > > My guess would be that this misses the compiler flags necessary to have > M_PI defined. The best way to get this working might be to let > simfactory also detect the cluster configuration on the compute nodes > (where you compile), such that setup-silent is not needed, but instead > the correct cluster configuration is found and used automatically. In > order to do that, look at examples of 'aliaspattern' in the mdb/machines > directory. An alternative would be to tell simfactory specifically that > you want to use your machine configuration file. > > As a side-note: I noticed the command 'patch' is missing too. This is a > tool so common that it should be installed everywhere. Your admin is > probably the best person to ask for advise here. It should not be too > hard to install yourself, but that should not be necessary either, > especially when you are told to compile on compute nodes. > > Frank > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrandt at cct.lsu.edu Wed May 3 09:32:52 2023 From: sbrandt at cct.lsu.edu (Steven Brandt) Date: Wed, 3 May 2023 09:32:52 -0500 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: Message-ID: I notice from the output that your compiler claims "limits.h" is missing. Possibly there's something wrong with your icc setup? Maybe you should try using gcc / gfortran instead. --Steve On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > Dear Frank, > > I added the alias pattern?for the computing nodes and now ETK can > detect the cluster (checked by asking "whoami") during the batch > queuing. I'll get in touch with the admins to include 'patch'. > > However, the problem still persists, having assured that the correct > machine file and option list?are being used during the compilation. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Wed, May 3, 2023 at 3:49?PM Frank Loeffler > wrote: > > Hi Shamim > > On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: > >We are trying to compile ETK on ParamGanga at IIT Roorkee. The > >compilation > >stops at a very initial step and gives out the error: > > > >*checking whether the Fortran compiler (gfortran? ) works... > yeschecking > >whether the Fortran compiler (gfortran? ) is a cross-compiler... > nochecking > >whether the Fortran compiler (gfortran? ) supports TYPE(*) for > >CCTK_PointerTo... yeschecking how to run the C preprocessor... > cppchecking > >for ANSI C header files... nochecking for C99 features... > yeschecking for > >M_PI... noconfigure: error: M_PI not defined. Try adding > -D_XOPEN_SOURCE to > >CPPFLAGS.* > > > >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not > help. This > >error is consistent if we set up using Intel Compiler (2020 or > 2019), or > >gcc (11 or 10). I have attached the outfile, error file, machine > script, > >and option lists for both cases (Intel and gcc) for any reference. > > > >Secondly, we are not allowed to compile ETK on login nodes. So we are > >queuing a job script, which upon execution, enters the Cactus > directory, > >does "setup-silent", and then executes the build command. Is this > the right > >way to compile ETK using the batch script? Or should we do something > >different? I have attached the shell script (compile.sh) used for > sbatch > >queue for reference. > > I might be wrong, but setup-silent will not use your machine file > which > contains all the compiler flags, but will setup something "from > scratch" > instead. According to the logs, this will be, e.g., in > > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > > My guess would be that this misses the compiler flags necessary to > have > M_PI defined. The best way to get this working might be to let > simfactory also detect the cluster configuration on the compute nodes > (where you compile), such that setup-silent is not needed, but > instead > the correct cluster configuration is found and used automatically. In > order to do that, look at examples of 'aliaspattern' in the > mdb/machines > directory. An alternative would be to tell simfactory specifically > that > you want to use your machine configuration file. > > As a side-note: I noticed the command 'patch' is missing too. This > is a > tool so common that it should be installed everywhere. Your admin is > probably the best person to ask for advise here. It should not be too > hard to install yourself, but that should not be necessary either, > especially when you are told to compile on compute nodes. > > Frank > > > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -------------- next part -------------- An HTML attachment was scrubbed... URL: From shamims at iiserb.ac.in Wed May 3 13:50:14 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Thu, 4 May 2023 00:20:14 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: Message-ID: Dear Steve, I tried gcc (10 and 11) as well and I am stuck with the following error: *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.* This also happened for Intel (2020 and 2019). I have attached both the output files here. Please ignore the out file in the first email, I have uploaded another out file by mistake. The rest of the files are correct in the first mail. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Wed, May 3, 2023 at 8:04?PM Steven Brandt wrote: > I notice from the output that your compiler claims "limits.h" is missing. > Possibly there's something wrong with your icc setup? Maybe you should try > using gcc / gfortran instead. > > --Steve > On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > > Dear Frank, > > I added the alias pattern for the computing nodes and now ETK can detect > the cluster (checked by asking "whoami") during the batch queuing. I'll get > in touch with the admins to include 'patch'. > > However, the problem still persists, having assured that the correct > machine file and option list are being used during the compilation. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Wed, May 3, 2023 at 3:49?PM Frank Loeffler > wrote: > >> Hi Shamim >> >> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: >> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The >> >compilation >> >stops at a very initial step and gives out the error: >> > >> >*checking whether the Fortran compiler (gfortran ) works... yeschecking >> >whether the Fortran compiler (gfortran ) is a cross-compiler... >> nochecking >> >whether the Fortran compiler (gfortran ) supports TYPE(*) for >> >CCTK_PointerTo... yeschecking how to run the C preprocessor... >> cppchecking >> >for ANSI C header files... nochecking for C99 features... yeschecking for >> >M_PI... noconfigure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE >> to >> >CPPFLAGS.* >> > >> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. This >> >error is consistent if we set up using Intel Compiler (2020 or 2019), or >> >gcc (11 or 10). I have attached the outfile, error file, machine script, >> >and option lists for both cases (Intel and gcc) for any reference. >> > >> >Secondly, we are not allowed to compile ETK on login nodes. So we are >> >queuing a job script, which upon execution, enters the Cactus directory, >> >does "setup-silent", and then executes the build command. Is this the >> right >> >way to compile ETK using the batch script? Or should we do something >> >different? I have attached the shell script (compile.sh) used for sbatch >> >queue for reference. >> >> I might be wrong, but setup-silent will not use your machine file which >> contains all the compiler flags, but will setup something "from scratch" >> instead. According to the logs, this will be, e.g., in >> >> >> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini >> >> My guess would be that this misses the compiler flags necessary to have >> M_PI defined. The best way to get this working might be to let >> simfactory also detect the cluster configuration on the compute nodes >> (where you compile), such that setup-silent is not needed, but instead >> the correct cluster configuration is found and used automatically. In >> order to do that, look at examples of 'aliaspattern' in the mdb/machines >> directory. An alternative would be to tell simfactory specifically that >> you want to use your machine configuration file. >> >> As a side-note: I noticed the command 'patch' is missing too. This is a >> tool so common that it should be installed everywhere. Your admin is >> probably the best person to ask for advise here. It should not be too >> hard to install yourself, but that should not be necessary either, >> especially when you are told to compile on compute nodes. >> >> Frank >> >> > _______________________________________________ > Users mailing listUsers at einsteintoolkit.orghttp://lists.einsteintoolkit.org/mailman/listinfo/users > > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: compile_intel.out Type: application/octet-stream Size: 5843 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: compile_gcc.out Type: application/octet-stream Size: 4832 bytes Desc: not available URL: From rhaas at illinois.edu Thu May 4 10:05:40 2023 From: rhaas at illinois.edu (Roland Haas) Date: Thu, 4 May 2023 10:05:40 -0500 Subject: [Users] meeting minutes for 2023-05-04 Message-ID: <20230504100540.4cf7e0b1@ekohaes8> Present: Roland, Peter, Zach, Gabriele, Leo, Sam ET release timeline =================== * release date will be May 24th * Leo and Sam are sending emails to the contributors and drafting the release announcement * inclusions are reviewed ok kuibit ====== * Gabriele finds that installing kuibit using pip is getting harder and coming up with generic instructions is difficult * Ubuntu 23.04 (and other new versions) prohibit use of `pip install --user` and strongly favor virtualenv * Also link required package instructions as described in https://bitbucket.org/einsteintoolkit/tickets/issues/2724/update-download-page Testsuite status ================ * no updates * test need to be re-run after fix to Fortran AliasedFunctions code * Peter will re-run on sunrise once release branches are in place * Roland has updated tests for Frontera and will re-run other tests * Anuj will re-run tests on thornyflat Gallery tests ============= BBH: no update BNS: Roland updated example TOV: Peter will run Multipatch: no update Poisson: no volunteer, Leo and Sam to look for people Gabriele suggested to have more detailed change list listing bugs more explicitly * Zach suggests using the script that shows changes for review by the release managers * Gabriele suggests providing a link to this information, also to resolved tickets * link to revolved and closed tickets sorted by date: https://bitbucket.org/einsteintoolkit/tickets/issues?status=resolved&status=invalid&status=closed&status=wontfix questions ========= * Gabriele mentioned large number of warning messages from Cactus when trying to run lean_public with presync_warn flags https://bitbucket.org/einsteintoolkit/tickets/issues/2723/no-boundary-conditions-registered-for ** there was some more generic discussion about how presync handles it various options * Leo brought up about HydroBaseX for CarpetX where currently there is no direct way to handle staggered variables ** this is more generic problem with variables that may sensibly be defined or used with different sorts of staggering. Current HydroBase assumes a single global choice is good enough for all codes that interface and that translation between representations is almost error free. emails ====== * existing emails by Shamim Haque, in conversation with Steve, ask Steve if is continuing the converstation tickets ======= * https://bitbucket.org/einsteintoolkit/tickets/issues/2722/getcomponents-places-kadaththorn-inside is needed for release, Roland will ask Steve chair next week: Zach minutes next week: Steve Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From rhaas at illinois.edu Thu May 11 09:49:05 2023 From: rhaas at illinois.edu (Roland Haas) Date: Thu, 11 May 2023 09:49:05 -0500 Subject: [Users] meeting minutes for 2023-05-11 Message-ID: <20230511094905.1d97d374@ekohaes8> Present: Roland, Peter, Zach, Jose, Keith, Sam, Steve, Leo, Johnny, Yosef ET release ========== * release managers will send out draft of release statement later today * 2 weeks to release, target date May 24th * no issues with remaining inclusions * Steve is asking for images to put on the release mug, Zach suggested looking for kuibit based images * Leo is not able to assign tickets on https://trac.einsteintoolkit.org, Roland will check if there is something off with his account compared to Sam, who can ET testsuite status =================== * Peter is compiling on db1 to run TOV star * Steve will run BBH * Roland has run BNS * Johnny has run Poisson equation, will update website * Multipatch scalar wave assigned to Jake (UTAusin), runs finished, working on uploading to website * Leo reduced runtime of NRPyEllipticET test and will push change Unanswered questions ==================== * Steve will contact Shamin Haque about issues on clusters * Zach suggested creating a "unanswered tickets" lists similar to unanswered questions. Roland says this should be possible with some Python code and REST API calls to bitbucket's API. Estimated work load is about 2hrs if one knows the API. * Leo will look into Tmunu ticket in Baikal https://bitbucket.org/einsteintoolkit/tickets/issues/2497/illinoisgrmhd-is-incompatible-with-setting * WENO coefficient ticket still up for review, will be done after release https://bitbucket.org/einsteintoolkit/tickets/issues/2647/incorrect-weno-coefficient-in-grhydro-weno ET summer school ================ * Registration is open, email is out * Travel support can be requested at registration time CarpetX ======= * Sam is asking about existing interpolation / deaverage code in CarpetX to from cell centered averages to samples or averages at cells, faces, vertices. Roland suggests that the prolongation operators could be used for some of this, but that most code so far seems to roll their own AEILocalInterp ============== * Roland and Zach looked into C auto-generating Maple code * Roland could re-run the scripts and re-generate the code * results looks identical up to renaming of variables and pass the current ET testsuites ** Roland noticed that 3d generation log files are missing, will check what is going on * Peter has 5th order Hermite codes for field to particle interpolation in GR-SPH code, will discuss with Zach if that can be made available * coeffs derived in MMA and code exported to Fortran from there Next chair: Sam Next minute taker: Steve Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From sbrandt at cct.lsu.edu Thu May 11 12:48:53 2023 From: sbrandt at cct.lsu.edu (Steven R. Brandt) Date: Thu, 11 May 2023 12:48:53 -0500 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> Message-ID: <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> I would talk to the system administrators about that. There is definitely something wrong with your compiler install if you can't find math.h. --Steve On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > Dear Steve, > > I just rechecked the cpp program to output M_PI in the computing > nodes, and that is not working right now, which was somehow working > fine a few days?ago. I also tried different?gcc versions (4.8, 10.2, > 11.1, gnu8/8.3) available in the cluster. All report similar issue: > > prog.cpp:1:18: fatal error: math.h: No such file or directory > ?#include > ? ? ? ? ? ? ? ? ? ^ > compilation terminated. > > ----OR----- > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > fatal error: features.h: No such file or directory > ? ?39 | #include > ? ? ? | ? ? ? ? ?^~~~~~~~~~~~ > compilation terminated. > > The?cpp code seems to work fine in login node, as it gives out the > value of pi upon execution. I am contacting the hpc admin to resolve > this?issue. > > I am attaching the test code (prog.cpp), the sbatch jobscript > (prog.sh) and the output file (slurn-117473.out), if you would like to > have a look at it. > > Please let me know if I should try something different to get this > working. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 > wrote: > > Thanks Steve. I'll make the changes and try again. I'll let you > know the outcome. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt > wrote: > > That tends to make me think you aren't using the compiler you > think you're using. You could put full paths in the .cfg files > and recompile from scratch. > > i.e. > > CXX = /full/path/to/icc > > --Steve > > On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: >> Yes, this gives the value of Pi successfully,?before starting >> the compilation: >> >> //home/vkerni.iitr/sam/trial >> 3.141593 >> Current machine: paramganga3 >> Using configuration: sim >> Reconfiguring sim >> Writing configuration to: >> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList >> Cactus - version: 4.12.0 >> Reconfiguring sim. >> / >> /./ >> /./ >> /./ >> /checking for M_PI... no >> configure: error: M_PI not defined. Try adding >> -D_XOPEN_SOURCE to CPPFLAGS. >> >> Error reconfiguring sim-config >> make: *** [sim-config] Error 2 >> / >> >> >> Shamim Haque >> Senior Research Fellow (SRF) >> Department of Physics >> IISER Bhopal >> >> ? >> >> On Thu, May 4, 2023 at 12:29?AM Steven Brandt >> wrote: >> >> So, sanity check, can you compile the following program >> outside of Cactus? >> >> #include >> #include >> >> int main() { >> ??? printf("%f\n", M_PI); >> ??? return 0; >> } >> >> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: >>> Dear Steve, >>> >>> I tried?gcc (10 and 11) as well and I am stuck with the >>> following error: >>> /configure: error: M_PI not defined. Try adding >>> -D_XOPEN_SOURCE to CPPFLAGS./ >>> / >>> / >>> This also happened for Intel (2020 and 2019). I >>> have?attached both the output files here. >>> >>> Please ignore the out file in the first email, I have >>> uploaded another out file by mistake. The rest of the >>> files are correct in the first mail. >>> >>> Regards >>> Shamim Haque >>> Senior Research Fellow (SRF) >>> Department of Physics >>> IISER Bhopal >>> >>> ? >>> >>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt >>> wrote: >>> >>> I notice from the output that your compiler claims >>> "limits.h" is missing. Possibly there's something >>> wrong with your icc setup? Maybe you should try >>> using gcc / gfortran instead. >>> >>> --Steve >>> >>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: >>>> Dear Frank, >>>> >>>> I added the alias pattern?for the computing nodes >>>> and now ETK can detect the cluster (checked by >>>> asking "whoami") during the batch queuing. I'll get >>>> in touch with the admins to include 'patch'. >>>> >>>> However, the problem still persists, having assured >>>> that the correct machine file and option list?are >>>> being used during the compilation. >>>> >>>> Regards >>>> Shamim Haque >>>> Senior Research Fellow (SRF) >>>> Department of Physics >>>> IISER Bhopal >>>> >>>> ? >>>> >>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler >>>> wrote: >>>> >>>> Hi Shamim >>>> >>>> On Wed, May 03, 2023 at 03:11:49PM +0530, >>>> Shamim Haque 1910511 wrote: >>>> >We are trying to compile ETK on ParamGanga at >>>> IIT Roorkee. The >>>> >compilation >>>> >stops at a very initial step and gives out the >>>> error: >>>> > >>>> >*checking whether the Fortran compiler >>>> (gfortran? ) works... yeschecking >>>> >whether the Fortran compiler (gfortran? ) is a >>>> cross-compiler... nochecking >>>> >whether the Fortran compiler (gfortran? ) >>>> supports TYPE(*) for >>>> >CCTK_PointerTo... yeschecking how to run the C >>>> preprocessor... cppchecking >>>> >for ANSI C header files... nochecking for C99 >>>> features... yeschecking for >>>> >M_PI... noconfigure: error: M_PI not defined. >>>> Try adding -D_XOPEN_SOURCE to >>>> >CPPFLAGS.* >>>> > >>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, >>>> but it does not help. This >>>> >error is consistent if we set up using Intel >>>> Compiler (2020 or 2019), or >>>> >gcc (11 or 10). I have attached the outfile, >>>> error file, machine script, >>>> >and option lists for both cases (Intel and >>>> gcc) for any reference. >>>> > >>>> >Secondly, we are not allowed to compile ETK on >>>> login nodes. So we are >>>> >queuing a job script, which upon execution, >>>> enters the Cactus directory, >>>> >does "setup-silent", and then executes the >>>> build command. Is this the right >>>> >way to compile ETK using the batch script? Or >>>> should we do something >>>> >different? I have attached the shell script >>>> (compile.sh) used for sbatch >>>> >queue for reference. >>>> >>>> I might be wrong, but setup-silent will not use >>>> your machine file which >>>> contains all the compiler flags, but will setup >>>> something "from scratch" >>>> instead. According to the logs, this will be, >>>> e.g., in >>>> >>>> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini >>>> >>>> My guess would be that this misses the compiler >>>> flags necessary to have >>>> M_PI defined. The best way to get this working >>>> might be to let >>>> simfactory also detect the cluster >>>> configuration on the compute nodes >>>> (where you compile), such that setup-silent is >>>> not needed, but instead >>>> the correct cluster configuration is found and >>>> used automatically. In >>>> order to do that, look at examples of >>>> 'aliaspattern' in the mdb/machines >>>> directory. An alternative would be to tell >>>> simfactory specifically that >>>> you want to use your machine configuration file. >>>> >>>> As a side-note: I noticed the command 'patch' >>>> is missing too. This is a >>>> tool so common that it should be installed >>>> everywhere. Your admin is >>>> probably the best person to ask for advise >>>> here. It should not be too >>>> hard to install yourself, but that should not >>>> be necessary either, >>>> especially when you are told to compile on >>>> compute nodes. >>>> >>>> Frank >>>> >>>> >>>> _______________________________________________ >>>> Users mailing list >>>> Users at einsteintoolkit.org >>>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>> _______________________________________________ >>> Users mailing list >>> Users at einsteintoolkit.org >>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From shamims at iiserb.ac.in Thu May 11 12:54:33 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Thu, 11 May 2023 23:24:33 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> Message-ID: Thanks Steve. I have raised complaint to the admin about this issue. On Thu, May 11, 2023, 11:18 PM Steven R. Brandt wrote: > I would talk to the system administrators about that. There is definitely > something wrong with your compiler install if you can't find math.h. > > --Steve > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > > Dear Steve, > > I just rechecked the cpp program to output M_PI in the computing nodes, > and that is not working right now, which was somehow working fine a few > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, gnu8/8.3) > available in the cluster. All report similar issue: > > prog.cpp:1:18: fatal error: math.h: No such file or directory > #include > ^ > compilation terminated. > > ----OR----- > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > fatal error: features.h: No such file or directory > 39 | #include > | ^~~~~~~~~~~~ > compilation terminated. > > The cpp code seems to work fine in login node, as it gives out the value > of pi upon execution. I am contacting the hpc admin to resolve this issue. > > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh) > and the output file (slurn-117473.out), if you would like to have a look at > it. > > Please let me know if I should try something different to get this working. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 > wrote: > >> Thanks Steve. I'll make the changes and try again. I'll let you know the >> outcome. >> >> Regards >> Shamim Haque >> Senior Research Fellow (SRF) >> Department of Physics >> IISER Bhopal >> >> ? >> >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt >> wrote: >> >>> That tends to make me think you aren't using the compiler you think >>> you're using. You could put full paths in the .cfg files and recompile from >>> scratch. >>> >>> i.e. >>> >>> CXX = /full/path/to/icc >>> >>> --Steve >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: >>> >>> Yes, this gives the value of Pi successfully, before starting the >>> compilation: >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 Using >>> configuration: sim Reconfiguring sim Writing configuration to: >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus - >>> version: 4.12.0 Reconfiguring sim. * >>> *.* >>> *.* >>> *.* >>> >>> >>> >>> >>> >>> *checking for M_PI... no configure: error: M_PI not defined. Try adding >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: *** >>> [sim-config] Error 2 * >>> >>> >>> Shamim Haque >>> Senior Research Fellow (SRF) >>> Department of Physics >>> IISER Bhopal >>> >>> ? >>> >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt >>> wrote: >>> >>>> So, sanity check, can you compile the following program outside of >>>> Cactus? >>>> >>>> #include >>>> #include >>>> >>>> int main() { >>>> printf("%f\n", M_PI); >>>> return 0; >>>> } >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: >>>> >>>> Dear Steve, >>>> >>>> I tried gcc (10 and 11) as well and I am stuck with the following error: >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to >>>> CPPFLAGS.* >>>> >>>> This also happened for Intel (2020 and 2019). I have attached both the >>>> output files here. >>>> >>>> Please ignore the out file in the first email, I have uploaded another >>>> out file by mistake. The rest of the files are correct in the first mail. >>>> >>>> Regards >>>> Shamim Haque >>>> Senior Research Fellow (SRF) >>>> Department of Physics >>>> IISER Bhopal >>>> >>>> ? >>>> >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt >>>> wrote: >>>> >>>>> I notice from the output that your compiler claims "limits.h" is >>>>> missing. Possibly there's something wrong with your icc setup? Maybe you >>>>> should try using gcc / gfortran instead. >>>>> >>>>> --Steve >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: >>>>> >>>>> Dear Frank, >>>>> >>>>> I added the alias pattern for the computing nodes and now ETK can >>>>> detect the cluster (checked by asking "whoami") during the batch queuing. >>>>> I'll get in touch with the admins to include 'patch'. >>>>> >>>>> However, the problem still persists, having assured that the correct >>>>> machine file and option list are being used during the compilation. >>>>> >>>>> Regards >>>>> Shamim Haque >>>>> Senior Research Fellow (SRF) >>>>> Department of Physics >>>>> IISER Bhopal >>>>> >>>>> ? >>>>> >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < >>>>> frank.loeffler at uni-jena.de> wrote: >>>>> >>>>>> Hi Shamim >>>>>> >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The >>>>>> >compilation >>>>>> >stops at a very initial step and gives out the error: >>>>>> > >>>>>> >*checking whether the Fortran compiler (gfortran ) works... >>>>>> yeschecking >>>>>> >whether the Fortran compiler (gfortran ) is a cross-compiler... >>>>>> nochecking >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... >>>>>> cppchecking >>>>>> >for ANSI C header files... nochecking for C99 features... >>>>>> yeschecking for >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding >>>>>> -D_XOPEN_SOURCE to >>>>>> >CPPFLAGS.* >>>>>> > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. >>>>>> This >>>>>> >error is consistent if we set up using Intel Compiler (2020 or >>>>>> 2019), or >>>>>> >gcc (11 or 10). I have attached the outfile, error file, machine >>>>>> script, >>>>>> >and option lists for both cases (Intel and gcc) for any reference. >>>>>> > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. So we are >>>>>> >queuing a job script, which upon execution, enters the Cactus >>>>>> directory, >>>>>> >does "setup-silent", and then executes the build command. Is this >>>>>> the right >>>>>> >way to compile ETK using the batch script? Or should we do something >>>>>> >different? I have attached the shell script (compile.sh) used for >>>>>> sbatch >>>>>> >queue for reference. >>>>>> >>>>>> I might be wrong, but setup-silent will not use your machine file >>>>>> which >>>>>> contains all the compiler flags, but will setup something "from >>>>>> scratch" >>>>>> instead. According to the logs, this will be, e.g., in >>>>>> >>>>>> >>>>>> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini >>>>>> >>>>>> My guess would be that this misses the compiler flags necessary to >>>>>> have >>>>>> M_PI defined. The best way to get this working might be to let >>>>>> simfactory also detect the cluster configuration on the compute nodes >>>>>> (where you compile), such that setup-silent is not needed, but >>>>>> instead >>>>>> the correct cluster configuration is found and used automatically. In >>>>>> order to do that, look at examples of 'aliaspattern' in the >>>>>> mdb/machines >>>>>> directory. An alternative would be to tell simfactory specifically >>>>>> that >>>>>> you want to use your machine configuration file. >>>>>> >>>>>> As a side-note: I noticed the command 'patch' is missing too. This is >>>>>> a >>>>>> tool so common that it should be installed everywhere. Your admin is >>>>>> probably the best person to ask for advise here. It should not be too >>>>>> hard to install yourself, but that should not be necessary either, >>>>>> especially when you are told to compile on compute nodes. >>>>>> >>>>>> Frank >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Users mailing listUsers at einsteintoolkit.orghttp://lists.einsteintoolkit.org/mailman/listinfo/users >>>>> >>>>> _______________________________________________ >>>>> Users mailing list >>>>> Users at einsteintoolkit.org >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhaas at illinois.edu Thu May 11 13:50:18 2023 From: rhaas at illinois.edu (Roland Haas) Date: Thu, 11 May 2023 13:50:18 -0500 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> Message-ID: <20230511135018.1d31cfb1@ekohaes8> Hello all, Since the error is a missing M_PI and the configure script already gives a suggested fix: Try adding -D_XOPEN_SOURCE to CPPFLAGS. have you tried adding: CPPFLAGS=-D_XOPEN_SOURCE to your option list file before compiling? Yours, Roland > Thanks Steve. I have raised complaint to the admin about this issue. > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt wrote: > > > I would talk to the system administrators about that. There is definitely > > something wrong with your compiler install if you can't find math.h. > > > > --Steve > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > > > > Dear Steve, > > > > I just rechecked the cpp program to output M_PI in the computing nodes, > > and that is not working right now, which was somehow working fine a few > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, gnu8/8.3) > > available in the cluster. All report similar issue: > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory > > #include > > ^ > > compilation terminated. > > > > ----OR----- > > > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > > fatal error: features.h: No such file or directory > > 39 | #include > > | ^~~~~~~~~~~~ > > compilation terminated. > > > > The cpp code seems to work fine in login node, as it gives out the value > > of pi upon execution. I am contacting the hpc admin to resolve this issue. > > > > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh) > > and the output file (slurn-117473.out), if you would like to have a look at > > it. > > > > Please let me know if I should try something different to get this working. > > > > Regards > > Shamim Haque > > Senior Research Fellow (SRF) > > Department of Physics > > IISER Bhopal > > > > ? > > > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 > > wrote: > > > >> Thanks Steve. I'll make the changes and try again. I'll let you know the > >> outcome. > >> > >> Regards > >> Shamim Haque > >> Senior Research Fellow (SRF) > >> Department of Physics > >> IISER Bhopal > >> > >> ? > >> > >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt > >> wrote: > >> > >>> That tends to make me think you aren't using the compiler you think > >>> you're using. You could put full paths in the .cfg files and recompile from > >>> scratch. > >>> > >>> i.e. > >>> > >>> CXX = /full/path/to/icc > >>> > >>> --Steve > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: > >>> > >>> Yes, this gives the value of Pi successfully, before starting the > >>> compilation: > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 Using > >>> configuration: sim Reconfiguring sim Writing configuration to: > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus - > >>> version: 4.12.0 Reconfiguring sim. * > >>> *.* > >>> *.* > >>> *.* > >>> > >>> > >>> > >>> > >>> > >>> *checking for M_PI... no configure: error: M_PI not defined. Try adding > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: *** > >>> [sim-config] Error 2 * > >>> > >>> > >>> Shamim Haque > >>> Senior Research Fellow (SRF) > >>> Department of Physics > >>> IISER Bhopal > >>> > >>> ? > >>> > >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt > >>> wrote: > >>> > >>>> So, sanity check, can you compile the following program outside of > >>>> Cactus? > >>>> > >>>> #include > >>>> #include > >>>> > >>>> int main() { > >>>> printf("%f\n", M_PI); > >>>> return 0; > >>>> } > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: > >>>> > >>>> Dear Steve, > >>>> > >>>> I tried gcc (10 and 11) as well and I am stuck with the following error: > >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to > >>>> CPPFLAGS.* > >>>> > >>>> This also happened for Intel (2020 and 2019). I have attached both the > >>>> output files here. > >>>> > >>>> Please ignore the out file in the first email, I have uploaded another > >>>> out file by mistake. The rest of the files are correct in the first mail. > >>>> > >>>> Regards > >>>> Shamim Haque > >>>> Senior Research Fellow (SRF) > >>>> Department of Physics > >>>> IISER Bhopal > >>>> > >>>> ? > >>>> > >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt > >>>> wrote: > >>>> > >>>>> I notice from the output that your compiler claims "limits.h" is > >>>>> missing. Possibly there's something wrong with your icc setup? Maybe you > >>>>> should try using gcc / gfortran instead. > >>>>> > >>>>> --Steve > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > >>>>> > >>>>> Dear Frank, > >>>>> > >>>>> I added the alias pattern for the computing nodes and now ETK can > >>>>> detect the cluster (checked by asking "whoami") during the batch queuing. > >>>>> I'll get in touch with the admins to include 'patch'. > >>>>> > >>>>> However, the problem still persists, having assured that the correct > >>>>> machine file and option list are being used during the compilation. > >>>>> > >>>>> Regards > >>>>> Shamim Haque > >>>>> Senior Research Fellow (SRF) > >>>>> Department of Physics > >>>>> IISER Bhopal > >>>>> > >>>>> ? > >>>>> > >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < > >>>>> frank.loeffler at uni-jena.de> wrote: > >>>>> > >>>>>> Hi Shamim > >>>>>> > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote: > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The > >>>>>> >compilation > >>>>>> >stops at a very initial step and gives out the error: > >>>>>> > > >>>>>> >*checking whether the Fortran compiler (gfortran ) works... > >>>>>> yeschecking > >>>>>> >whether the Fortran compiler (gfortran ) is a cross-compiler... > >>>>>> nochecking > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for > >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... > >>>>>> cppchecking > >>>>>> >for ANSI C header files... nochecking for C99 features... > >>>>>> yeschecking for > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding > >>>>>> -D_XOPEN_SOURCE to > >>>>>> >CPPFLAGS.* > >>>>>> > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. > >>>>>> This > >>>>>> >error is consistent if we set up using Intel Compiler (2020 or > >>>>>> 2019), or > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, machine > >>>>>> script, > >>>>>> >and option lists for both cases (Intel and gcc) for any reference. > >>>>>> > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. So we are > >>>>>> >queuing a job script, which upon execution, enters the Cactus > >>>>>> directory, > >>>>>> >does "setup-silent", and then executes the build command. Is this > >>>>>> the right > >>>>>> >way to compile ETK using the batch script? Or should we do something > >>>>>> >different? I have attached the shell script (compile.sh) used for > >>>>>> sbatch > >>>>>> >queue for reference. > >>>>>> > >>>>>> I might be wrong, but setup-silent will not use your machine file > >>>>>> which > >>>>>> contains all the compiler flags, but will setup something "from > >>>>>> scratch" > >>>>>> instead. According to the logs, this will be, e.g., in > >>>>>> > >>>>>> > >>>>>> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > >>>>>> > >>>>>> My guess would be that this misses the compiler flags necessary to > >>>>>> have > >>>>>> M_PI defined. The best way to get this working might be to let > >>>>>> simfactory also detect the cluster configuration on the compute nodes > >>>>>> (where you compile), such that setup-silent is not needed, but > >>>>>> instead > >>>>>> the correct cluster configuration is found and used automatically. In > >>>>>> order to do that, look at examples of 'aliaspattern' in the > >>>>>> mdb/machines > >>>>>> directory. An alternative would be to tell simfactory specifically > >>>>>> that > >>>>>> you want to use your machine configuration file. > >>>>>> > >>>>>> As a side-note: I noticed the command 'patch' is missing too. This is > >>>>>> a > >>>>>> tool so common that it should be installed everywhere. Your admin is > >>>>>> probably the best person to ask for advise here. It should not be too > >>>>>> hard to install yourself, but that should not be necessary either, > >>>>>> especially when you are told to compile on compute nodes. > >>>>>> > >>>>>> Frank > >>>>>> > >>>>>> > >>>>> _______________________________________________ > >>>>> Users mailing listUsers at einsteintoolkit.orghttp://lists.einsteintoolkit.org/mailman/listinfo/users > >>>>> > >>>>> _______________________________________________ > >>>>> Users mailing list > >>>>> Users at einsteintoolkit.org > >>>>> https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$ > >>>>> > >>>> Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From shamims at iiserb.ac.in Thu May 11 15:28:33 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Fri, 12 May 2023 01:58:33 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: <20230511135018.1d31cfb1@ekohaes8> References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> <20230511135018.1d31cfb1@ekohaes8> Message-ID: Hello Roland, I did try that fix; the error remains the same. Actually, we landed on an even more primitive problem, where Steve suggested a basic test, that is to compile the following code: *#include #include int main() { printf("%f\n", M_PI); return 0;}* This program compiles just fine in the login node but gives out the following error while compiling it via jobscript submission in the sbatch queue: prog.cpp:1:18: fatal error: math.h: No such file or directory #include ^ compilation terminated. ----OR----- /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: fatal error: features.h: No such file or directory 39 | #include | ^~~~~~~~~~~~ compilation terminated. I have reported this problem to the HPC admin and await their response. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Fri, May 12, 2023 at 12:20?AM Roland Haas wrote: > Hello all, > > Since the error is a missing M_PI and the configure script already > gives a suggested fix: > > Try adding -D_XOPEN_SOURCE to CPPFLAGS. > > have you tried adding: > > CPPFLAGS=-D_XOPEN_SOURCE > > to your option list file before compiling? > > Yours, > Roland > > > Thanks Steve. I have raised complaint to the admin about this issue. > > > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt > wrote: > > > > > I would talk to the system administrators about that. There is > definitely > > > something wrong with your compiler install if you can't find math.h. > > > > > > --Steve > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > > > > > > Dear Steve, > > > > > > I just rechecked the cpp program to output M_PI in the computing nodes, > > > and that is not working right now, which was somehow working fine a few > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, > gnu8/8.3) > > > available in the cluster. All report similar issue: > > > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory > > > #include > > > ^ > > > compilation terminated. > > > > > > ----OR----- > > > > > > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > > > fatal error: features.h: No such file or directory > > > 39 | #include > > > | ^~~~~~~~~~~~ > > > compilation terminated. > > > > > > The cpp code seems to work fine in login node, as it gives out the > value > > > of pi upon execution. I am contacting the hpc admin to resolve this > issue. > > > > > > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh) > > > and the output file (slurn-117473.out), if you would like to have a > look at > > > it. > > > > > > Please let me know if I should try something different to get this > working. > > > > > > Regards > > > Shamim Haque > > > Senior Research Fellow (SRF) > > > Department of Physics > > > IISER Bhopal > > > > > > ? > > > > > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 < > shamims at iiserb.ac.in> > > > wrote: > > > > > >> Thanks Steve. I'll make the changes and try again. I'll let you know > the > > >> outcome. > > >> > > >> Regards > > >> Shamim Haque > > >> Senior Research Fellow (SRF) > > >> Department of Physics > > >> IISER Bhopal > > >> > > >> ? > > >> > > >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt > > >> wrote: > > >> > > >>> That tends to make me think you aren't using the compiler you think > > >>> you're using. You could put full paths in the .cfg files and > recompile from > > >>> scratch. > > >>> > > >>> i.e. > > >>> > > >>> CXX = /full/path/to/icc > > >>> > > >>> --Steve > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: > > >>> > > >>> Yes, this gives the value of Pi successfully, before starting the > > >>> compilation: > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 > Using > > >>> configuration: sim Reconfiguring sim Writing configuration to: > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus - > > >>> version: 4.12.0 Reconfiguring sim. * > > >>> *.* > > >>> *.* > > >>> *.* > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> *checking for M_PI... no configure: error: M_PI not defined. Try > adding > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: *** > > >>> [sim-config] Error 2 * > > >>> > > >>> > > >>> Shamim Haque > > >>> Senior Research Fellow (SRF) > > >>> Department of Physics > > >>> IISER Bhopal > > >>> > > >>> ? > > >>> > > >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt > > >>> wrote: > > >>> > > >>>> So, sanity check, can you compile the following program outside of > > >>>> Cactus? > > >>>> > > >>>> #include > > >>>> #include > > >>>> > > >>>> int main() { > > >>>> printf("%f\n", M_PI); > > >>>> return 0; > > >>>> } > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: > > >>>> > > >>>> Dear Steve, > > >>>> > > >>>> I tried gcc (10 and 11) as well and I am stuck with the following > error: > > >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to > > >>>> CPPFLAGS.* > > >>>> > > >>>> This also happened for Intel (2020 and 2019). I have attached both > the > > >>>> output files here. > > >>>> > > >>>> Please ignore the out file in the first email, I have uploaded > another > > >>>> out file by mistake. The rest of the files are correct in the first > mail. > > >>>> > > >>>> Regards > > >>>> Shamim Haque > > >>>> Senior Research Fellow (SRF) > > >>>> Department of Physics > > >>>> IISER Bhopal > > >>>> > > >>>> ? > > >>>> > > >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt > > >>>> wrote: > > >>>> > > >>>>> I notice from the output that your compiler claims "limits.h" is > > >>>>> missing. Possibly there's something wrong with your icc setup? > Maybe you > > >>>>> should try using gcc / gfortran instead. > > >>>>> > > >>>>> --Steve > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > > >>>>> > > >>>>> Dear Frank, > > >>>>> > > >>>>> I added the alias pattern for the computing nodes and now ETK can > > >>>>> detect the cluster (checked by asking "whoami") during the batch > queuing. > > >>>>> I'll get in touch with the admins to include 'patch'. > > >>>>> > > >>>>> However, the problem still persists, having assured that the > correct > > >>>>> machine file and option list are being used during the compilation. > > >>>>> > > >>>>> Regards > > >>>>> Shamim Haque > > >>>>> Senior Research Fellow (SRF) > > >>>>> Department of Physics > > >>>>> IISER Bhopal > > >>>>> > > >>>>> ? > > >>>>> > > >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < > > >>>>> frank.loeffler at uni-jena.de> wrote: > > >>>>> > > >>>>>> Hi Shamim > > >>>>>> > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 > wrote: > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The > > >>>>>> >compilation > > >>>>>> >stops at a very initial step and gives out the error: > > >>>>>> > > > >>>>>> >*checking whether the Fortran compiler (gfortran ) works... > > >>>>>> yeschecking > > >>>>>> >whether the Fortran compiler (gfortran ) is a > cross-compiler... > > >>>>>> nochecking > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... > > >>>>>> cppchecking > > >>>>>> >for ANSI C header files... nochecking for C99 features... > > >>>>>> yeschecking for > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding > > >>>>>> -D_XOPEN_SOURCE to > > >>>>>> >CPPFLAGS.* > > >>>>>> > > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not > help. > > >>>>>> This > > >>>>>> >error is consistent if we set up using Intel Compiler (2020 or > > >>>>>> 2019), or > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, > machine > > >>>>>> script, > > >>>>>> >and option lists for both cases (Intel and gcc) for any > reference. > > >>>>>> > > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. So > we are > > >>>>>> >queuing a job script, which upon execution, enters the Cactus > > >>>>>> directory, > > >>>>>> >does "setup-silent", and then executes the build command. Is > this > > >>>>>> the right > > >>>>>> >way to compile ETK using the batch script? Or should we do > something > > >>>>>> >different? I have attached the shell script (compile.sh) used > for > > >>>>>> sbatch > > >>>>>> >queue for reference. > > >>>>>> > > >>>>>> I might be wrong, but setup-silent will not use your machine file > > >>>>>> which > > >>>>>> contains all the compiler flags, but will setup something "from > > >>>>>> scratch" > > >>>>>> instead. According to the logs, this will be, e.g., in > > >>>>>> > > >>>>>> > > >>>>>> > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > > >>>>>> > > >>>>>> My guess would be that this misses the compiler flags necessary to > > >>>>>> have > > >>>>>> M_PI defined. The best way to get this working might be to let > > >>>>>> simfactory also detect the cluster configuration on the compute > nodes > > >>>>>> (where you compile), such that setup-silent is not needed, but > > >>>>>> instead > > >>>>>> the correct cluster configuration is found and used > automatically. In > > >>>>>> order to do that, look at examples of 'aliaspattern' in the > > >>>>>> mdb/machines > > >>>>>> directory. An alternative would be to tell simfactory specifically > > >>>>>> that > > >>>>>> you want to use your machine configuration file. > > >>>>>> > > >>>>>> As a side-note: I noticed the command 'patch' is missing too. > This is > > >>>>>> a > > >>>>>> tool so common that it should be installed everywhere. Your admin > is > > >>>>>> probably the best person to ask for advise here. It should not be > too > > >>>>>> hard to install yourself, but that should not be necessary either, > > >>>>>> especially when you are told to compile on compute nodes. > > >>>>>> > > >>>>>> Frank > > >>>>>> > > >>>>>> > > >>>>> _______________________________________________ > > >>>>> Users mailing listUsers at einsteintoolkit.orghttp:// > lists.einsteintoolkit.org/mailman/listinfo/users > > >>>>> > > >>>>> _______________________________________________ > > >>>>> Users mailing list > > >>>>> Users at einsteintoolkit.org > > >>>>> > https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$ > > >>>>> > > >>>> > > > Yours, > Roland > > -- > My email is as private as my paper mail. I therefore support encrypting > and signing email messages. Get my PGP key from http://pgp.mit.edu . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From piosif at auth.gr Wed May 17 10:29:33 2023 From: piosif at auth.gr (Panagiotis Iosif) Date: Wed, 17 May 2023 18:29:33 +0300 Subject: [Users] GetComponents "enqueue" error Message-ID: Dear ET users, I am trying to install ET on our local university cluster. I downloaded GetComponents and made it executable: curl -kLO https://raw.githubusercontent.com/gridaphobe/CRL/ET_2022_11/GetComponents chmod a+x GetComponents On the next step, when running the command: ./GetComponents --parallel https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2022_11/einsteintoolkit.th I get the following error and the process stops. "Can't call method "enqueue" on an undefined value at ./GetComponents line 1040." Do you have any insight on this? Best regards, Panagiotis ------------------------------------------------------------- Dr. Panagiotis Iosif postdoctoral researcher email: piosif at auth.gr; paniosif at gmail.com Section of Astrophysics, Astronomy and Mechanics Department of Physics Aristotle University of Thessaloniki 54124, Thessaloniki, Greece ------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhaas at illinois.edu Wed May 17 11:57:05 2023 From: rhaas at illinois.edu (Roland Haas) Date: Wed, 17 May 2023 11:57:05 -0500 Subject: [Users] GetComponents "enqueue" error In-Reply-To: References: Message-ID: <20230517115705.26b5798d@eduroamprvnat-172-16-54-7.near.illinois.edu> Hello Panagiotis, My guess would be a broken Perl install on the cluster. Can you try if you use --no-parallel instead? This may be a bit slower, but not by too much really. I would also check that the file einsteintoolkit.th that is downloaded (and shouold be in the same directory you were in when running GetComponents) is in fact not empty and is a valid ET thornlist (and not eg some HTML page with an error message, or an empty file). Yours, Roland On Wed, 17 May 2023 18:29:33 +0300 Panagiotis Iosif wrote: > Dear ET users, > > I am trying to install ET on our local university cluster. > > I downloaded GetComponents and made it executable: > curl -kLO > https://urldefense.com/v3/__https://raw.githubusercontent.com/gridaphobe/CRL/ET_2022_11/GetComponents__;!!DZ3fjg!_64zf46I-IsCEywhkt9D7iHlMwyoyJdt542DSYeSlaMlLrdEVYNMYrfrBd8V1G_HiaXsmJ3jE28640A$ > chmod a+x GetComponents > > On the next step, when running the command: > ./GetComponents --parallel > https://urldefense.com/v3/__https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2022_11/einsteintoolkit.th__;!!DZ3fjg!_64zf46I-IsCEywhkt9D7iHlMwyoyJdt542DSYeSlaMlLrdEVYNMYrfrBd8V1G_HiaXsmJ3j5EsbPOE$ > > I get the following error and the process stops. > "Can't call method "enqueue" on an undefined value at ./GetComponents > line 1040." > > Do you have any insight on this? > > Best regards, > Panagiotis > > ------------------------------------------------------------- > Dr. Panagiotis Iosif > postdoctoral researcher > email: piosif at auth.gr; paniosif at gmail.com > > Section of Astrophysics, Astronomy and Mechanics > Department of Physics > Aristotle University of Thessaloniki > 54124, Thessaloniki, Greece > ------------------------------------------------------------- From rhaas at illinois.edu Thu May 18 09:01:47 2023 From: rhaas at illinois.edu (Roland Haas) Date: Thu, 18 May 2023 09:01:47 -0500 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> <20230511135018.1d31cfb1@ekohaes8> Message-ID: <20230518090147.4248b227@ekohaes8> Hello Shamin, A missing math.h would point to a faulty compiler installation. Since you are trying to compile (are you?) ona compute node in a running job, my guess would be that the cluster admins are not providing compilers on the compute nodes but only on the login nodes. This would be something to contact your cluster's help desk about. Yours, Roland > Hello Roland, > > I did try that fix; the error remains the same. Actually, we landed on an > even more primitive problem, where Steve suggested a basic test, that is to > compile the following code: > > > > > > > > *#include #include int main() { printf("%f\n", > M_PI); return 0;}* > > This program compiles just fine in the login node but gives out the > following error while compiling it via jobscript submission in the sbatch > queue: > > prog.cpp:1:18: fatal error: math.h: No such file or directory > #include > ^ > compilation terminated. > > ----OR----- > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > fatal error: features.h: No such file or directory > 39 | #include > | ^~~~~~~~~~~~ > compilation terminated. > > I have reported this problem to the HPC admin and await their response. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Fri, May 12, 2023 at 12:20?AM Roland Haas wrote: > > > Hello all, > > > > Since the error is a missing M_PI and the configure script already > > gives a suggested fix: > > > > Try adding -D_XOPEN_SOURCE to CPPFLAGS. > > > > have you tried adding: > > > > CPPFLAGS=-D_XOPEN_SOURCE > > > > to your option list file before compiling? > > > > Yours, > > Roland > > > > > Thanks Steve. I have raised complaint to the admin about this issue. > > > > > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt > > wrote: > > > > > > > I would talk to the system administrators about that. There is > > definitely > > > > something wrong with your compiler install if you can't find math.h. > > > > > > > > --Steve > > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > > > > > > > > Dear Steve, > > > > > > > > I just rechecked the cpp program to output M_PI in the computing nodes, > > > > and that is not working right now, which was somehow working fine a few > > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, > > gnu8/8.3) > > > > available in the cluster. All report similar issue: > > > > > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory > > > > #include > > > > ^ > > > > compilation terminated. > > > > > > > > ----OR----- > > > > > > > > > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > > > > fatal error: features.h: No such file or directory > > > > 39 | #include > > > > | ^~~~~~~~~~~~ > > > > compilation terminated. > > > > > > > > The cpp code seems to work fine in login node, as it gives out the > > value > > > > of pi upon execution. I am contacting the hpc admin to resolve this > > issue. > > > > > > > > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh) > > > > and the output file (slurn-117473.out), if you would like to have a > > look at > > > > it. > > > > > > > > Please let me know if I should try something different to get this > > working. > > > > > > > > Regards > > > > Shamim Haque > > > > Senior Research Fellow (SRF) > > > > Department of Physics > > > > IISER Bhopal > > > > > > > > ? > > > > > > > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 < > > shamims at iiserb.ac.in> > > > > wrote: > > > > > > > >> Thanks Steve. I'll make the changes and try again. I'll let you know > > the > > > >> outcome. > > > >> > > > >> Regards > > > >> Shamim Haque > > > >> Senior Research Fellow (SRF) > > > >> Department of Physics > > > >> IISER Bhopal > > > >> > > > >> ? > > > >> > > > >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt > > > >> wrote: > > > >> > > > >>> That tends to make me think you aren't using the compiler you think > > > >>> you're using. You could put full paths in the .cfg files and > > recompile from > > > >>> scratch. > > > >>> > > > >>> i.e. > > > >>> > > > >>> CXX = /full/path/to/icc > > > >>> > > > >>> --Steve > > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: > > > >>> > > > >>> Yes, this gives the value of Pi successfully, before starting the > > > >>> compilation: > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 > > Using > > > >>> configuration: sim Reconfiguring sim Writing configuration to: > > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus - > > > >>> version: 4.12.0 Reconfiguring sim. * > > > >>> *.* > > > >>> *.* > > > >>> *.* > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> *checking for M_PI... no configure: error: M_PI not defined. Try > > adding > > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: *** > > > >>> [sim-config] Error 2 * > > > >>> > > > >>> > > > >>> Shamim Haque > > > >>> Senior Research Fellow (SRF) > > > >>> Department of Physics > > > >>> IISER Bhopal > > > >>> > > > >>> ? > > > >>> > > > >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt > > > >>> wrote: > > > >>> > > > >>>> So, sanity check, can you compile the following program outside of > > > >>>> Cactus? > > > >>>> > > > >>>> #include > > > >>>> #include > > > >>>> > > > >>>> int main() { > > > >>>> printf("%f\n", M_PI); > > > >>>> return 0; > > > >>>> } > > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: > > > >>>> > > > >>>> Dear Steve, > > > >>>> > > > >>>> I tried gcc (10 and 11) as well and I am stuck with the following > > error: > > > >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to > > > >>>> CPPFLAGS.* > > > >>>> > > > >>>> This also happened for Intel (2020 and 2019). I have attached both > > the > > > >>>> output files here. > > > >>>> > > > >>>> Please ignore the out file in the first email, I have uploaded > > another > > > >>>> out file by mistake. The rest of the files are correct in the first > > mail. > > > >>>> > > > >>>> Regards > > > >>>> Shamim Haque > > > >>>> Senior Research Fellow (SRF) > > > >>>> Department of Physics > > > >>>> IISER Bhopal > > > >>>> > > > >>>> ? > > > >>>> > > > >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt > > > >>>> wrote: > > > >>>> > > > >>>>> I notice from the output that your compiler claims "limits.h" is > > > >>>>> missing. Possibly there's something wrong with your icc setup? > > Maybe you > > > >>>>> should try using gcc / gfortran instead. > > > >>>>> > > > >>>>> --Steve > > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > > > >>>>> > > > >>>>> Dear Frank, > > > >>>>> > > > >>>>> I added the alias pattern for the computing nodes and now ETK can > > > >>>>> detect the cluster (checked by asking "whoami") during the batch > > queuing. > > > >>>>> I'll get in touch with the admins to include 'patch'. > > > >>>>> > > > >>>>> However, the problem still persists, having assured that the > > correct > > > >>>>> machine file and option list are being used during the compilation. > > > >>>>> > > > >>>>> Regards > > > >>>>> Shamim Haque > > > >>>>> Senior Research Fellow (SRF) > > > >>>>> Department of Physics > > > >>>>> IISER Bhopal > > > >>>>> > > > >>>>> ? > > > >>>>> > > > >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < > > > >>>>> frank.loeffler at uni-jena.de> wrote: > > > >>>>> > > > >>>>>> Hi Shamim > > > >>>>>> > > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 > > wrote: > > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The > > > >>>>>> >compilation > > > >>>>>> >stops at a very initial step and gives out the error: > > > >>>>>> > > > > >>>>>> >*checking whether the Fortran compiler (gfortran ) works... > > > >>>>>> yeschecking > > > >>>>>> >whether the Fortran compiler (gfortran ) is a > > cross-compiler... > > > >>>>>> nochecking > > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for > > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... > > > >>>>>> cppchecking > > > >>>>>> >for ANSI C header files... nochecking for C99 features... > > > >>>>>> yeschecking for > > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding > > > >>>>>> -D_XOPEN_SOURCE to > > > >>>>>> >CPPFLAGS.* > > > >>>>>> > > > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not > > help. > > > >>>>>> This > > > >>>>>> >error is consistent if we set up using Intel Compiler (2020 or > > > >>>>>> 2019), or > > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, > > machine > > > >>>>>> script, > > > >>>>>> >and option lists for both cases (Intel and gcc) for any > > reference. > > > >>>>>> > > > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. So > > we are > > > >>>>>> >queuing a job script, which upon execution, enters the Cactus > > > >>>>>> directory, > > > >>>>>> >does "setup-silent", and then executes the build command. Is > > this > > > >>>>>> the right > > > >>>>>> >way to compile ETK using the batch script? Or should we do > > something > > > >>>>>> >different? I have attached the shell script (compile.sh) used > > for > > > >>>>>> sbatch > > > >>>>>> >queue for reference. > > > >>>>>> > > > >>>>>> I might be wrong, but setup-silent will not use your machine file > > > >>>>>> which > > > >>>>>> contains all the compiler flags, but will setup something "from > > > >>>>>> scratch" > > > >>>>>> instead. According to the logs, this will be, e.g., in > > > >>>>>> > > > >>>>>> > > > >>>>>> > > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > > > >>>>>> > > > >>>>>> My guess would be that this misses the compiler flags necessary to > > > >>>>>> have > > > >>>>>> M_PI defined. The best way to get this working might be to let > > > >>>>>> simfactory also detect the cluster configuration on the compute > > nodes > > > >>>>>> (where you compile), such that setup-silent is not needed, but > > > >>>>>> instead > > > >>>>>> the correct cluster configuration is found and used > > automatically. In > > > >>>>>> order to do that, look at examples of 'aliaspattern' in the > > > >>>>>> mdb/machines > > > >>>>>> directory. An alternative would be to tell simfactory specifically > > > >>>>>> that > > > >>>>>> you want to use your machine configuration file. > > > >>>>>> > > > >>>>>> As a side-note: I noticed the command 'patch' is missing too. > > This is > > > >>>>>> a > > > >>>>>> tool so common that it should be installed everywhere. Your admin > > is > > > >>>>>> probably the best person to ask for advise here. It should not be > > too > > > >>>>>> hard to install yourself, but that should not be necessary either, > > > >>>>>> especially when you are told to compile on compute nodes. > > > >>>>>> > > > >>>>>> Frank > > > >>>>>> > > > >>>>>> > > > >>>>> _______________________________________________ > > > >>>>> Users mailing listUsers at einsteintoolkit.orghttp:// > > lists.einsteintoolkit.org/mailman/listinfo/users > > > >>>>> > > > >>>>> _______________________________________________ > > > >>>>> Users mailing list > > > >>>>> Users at einsteintoolkit.org > > > >>>>> > > https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$ > > > >>>>> > > > >>>> > > > > > > Yours, > > Roland > > > > -- > > My email is as private as my paper mail. I therefore support encrypting > > and signing email messages. Get my PGP key from https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$ . > > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From sbrandt at cct.lsu.edu Thu May 18 10:01:01 2023 From: sbrandt at cct.lsu.edu (Steven Brandt) Date: Thu, 18 May 2023 10:01:01 -0500 Subject: [Users] Meeting minutes for 2023-05-18 Message-ID: Present: Steve, Sam, Yosef, Keith, Roland, Zach, Peter, Jose Chair: Sam Notes: Steve Release: Most of the branches and tags have been done. Gallery: Not all done (Steve forgot). Peter did 4 different resolutions. Roland is moving the tutorial server to github Only Steve, Erik, and Roland can push to the dockerhub Steve needs to run tests on LSU machines. Issue with ticket 2497. IGMHD also has a parameter that replictaes one in TmunuBase. IGMHD will be deprecated to be replaced by GrhaylET. GrhaylET has 90% code coverage. US ET summer school: Registration is open Tutorials have been arranged EU ET summer school. Spec should still be happening. Peter has a convergence plot for NSs. Possible mug image. Steve needs to reply to email Next week: Chair: Peter, Minute Taker: Sam From shamims at iiserb.ac.in Fri May 19 04:02:29 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Fri, 19 May 2023 14:32:29 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: <20230518090147.4248b227@ekohaes8> References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> <20230511135018.1d31cfb1@ekohaes8> <20230518090147.4248b227@ekohaes8> Message-ID: Hello Roland, Thank you for the reply. Yes, I am trying to compile ETK in the computing node via sbatch queue. I am in touch with the system admin to resolve the issue with the compilers. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Thu, May 18, 2023 at 7:32?PM Roland Haas wrote: > Hello Shamin, > > A missing math.h would point to a faulty compiler installation. Since > you are trying to compile (are you?) ona compute node in a running job, > my guess would be that the cluster admins are not providing compilers > on the compute nodes but only on the login nodes. > > This would be something to contact your cluster's help desk about. > > Yours, > Roland > > > Hello Roland, > > > > I did try that fix; the error remains the same. Actually, we landed on an > > even more primitive problem, where Steve suggested a basic test, that is > to > > compile the following code: > > > > > > > > > > > > > > > > *#include #include int main() { printf("%f\n", > > M_PI); return 0;}* > > > > This program compiles just fine in the login node but gives out the > > following error while compiling it via jobscript submission in the sbatch > > queue: > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory > > #include > > ^ > > compilation terminated. > > > > ----OR----- > > > > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > > fatal error: features.h: No such file or directory > > 39 | #include > > | ^~~~~~~~~~~~ > > compilation terminated. > > > > I have reported this problem to the HPC admin and await their response. > > > > Regards > > Shamim Haque > > Senior Research Fellow (SRF) > > Department of Physics > > IISER Bhopal > > > > ? > > > > On Fri, May 12, 2023 at 12:20?AM Roland Haas wrote: > > > > > Hello all, > > > > > > Since the error is a missing M_PI and the configure script already > > > gives a suggested fix: > > > > > > Try adding -D_XOPEN_SOURCE to CPPFLAGS. > > > > > > have you tried adding: > > > > > > CPPFLAGS=-D_XOPEN_SOURCE > > > > > > to your option list file before compiling? > > > > > > Yours, > > > Roland > > > > > > > Thanks Steve. I have raised complaint to the admin about this issue. > > > > > > > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt > > > > wrote: > > > > > > > > > I would talk to the system administrators about that. There is > > > definitely > > > > > something wrong with your compiler install if you can't find > math.h. > > > > > > > > > > --Steve > > > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: > > > > > > > > > > Dear Steve, > > > > > > > > > > I just rechecked the cpp program to output M_PI in the computing > nodes, > > > > > and that is not working right now, which was somehow working fine > a few > > > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, > > > gnu8/8.3) > > > > > available in the cluster. All report similar issue: > > > > > > > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory > > > > > #include > > > > > ^ > > > > > compilation terminated. > > > > > > > > > > ----OR----- > > > > > > > > > > > > > > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: > > > > > > fatal error: features.h: No such file or directory > > > > > 39 | #include > > > > > | ^~~~~~~~~~~~ > > > > > compilation terminated. > > > > > > > > > > The cpp code seems to work fine in login node, as it gives out > the > > > value > > > > > of pi upon execution. I am contacting the hpc admin to resolve > this > > > issue. > > > > > > > > > > I am attaching the test code (prog.cpp), the sbatch jobscript > (prog.sh) > > > > > and the output file (slurn-117473.out), if you would like to have > a > > > look at > > > > > it. > > > > > > > > > > Please let me know if I should try something different to get > this > > > working. > > > > > > > > > > Regards > > > > > Shamim Haque > > > > > Senior Research Fellow (SRF) > > > > > Department of Physics > > > > > IISER Bhopal > > > > > > > > > > ? > > > > > > > > > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 < > > > shamims at iiserb.ac.in> > > > > > wrote: > > > > > > > > > >> Thanks Steve. I'll make the changes and try again. I'll let you > know > > > the > > > > >> outcome. > > > > >> > > > > >> Regards > > > > >> Shamim Haque > > > > >> Senior Research Fellow (SRF) > > > > >> Department of Physics > > > > >> IISER Bhopal > > > > >> > > > > >> ? > > > > >> > > > > >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt < > sbrandt at cct.lsu.edu> > > > > >> wrote: > > > > >> > > > > >>> That tends to make me think you aren't using the compiler you > think > > > > >>> you're using. You could put full paths in the .cfg files and > > > recompile from > > > > >>> scratch. > > > > >>> > > > > >>> i.e. > > > > >>> > > > > >>> CXX = /full/path/to/icc > > > > >>> > > > > >>> --Steve > > > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: > > > > >>> > > > > >>> Yes, this gives the value of Pi successfully, before starting the > > > > >>> compilation: > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: > paramganga3 > > > Using > > > > >>> configuration: sim Reconfiguring sim Writing configuration to: > > > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList > Cactus - > > > > >>> version: 4.12.0 Reconfiguring sim. * > > > > >>> *.* > > > > >>> *.* > > > > >>> *.* > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> *checking for M_PI... no configure: error: M_PI not defined. > Try > > > adding > > > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config > make: *** > > > > >>> [sim-config] Error 2 * > > > > >>> > > > > >>> > > > > >>> Shamim Haque > > > > >>> Senior Research Fellow (SRF) > > > > >>> Department of Physics > > > > >>> IISER Bhopal > > > > >>> > > > > >>> ? > > > > >>> > > > > >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt < > sbrandt at cct.lsu.edu> > > > > >>> wrote: > > > > >>> > > > > >>>> So, sanity check, can you compile the following program outside > of > > > > >>>> Cactus? > > > > >>>> > > > > >>>> #include > > > > >>>> #include > > > > >>>> > > > > >>>> int main() { > > > > >>>> printf("%f\n", M_PI); > > > > >>>> return 0; > > > > >>>> } > > > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: > > > > >>>> > > > > >>>> Dear Steve, > > > > >>>> > > > > >>>> I tried gcc (10 and 11) as well and I am stuck with the > following > > > error: > > > > >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE > to > > > > >>>> CPPFLAGS.* > > > > >>>> > > > > >>>> This also happened for Intel (2020 and 2019). I have attached > both > > > the > > > > >>>> output files here. > > > > >>>> > > > > >>>> Please ignore the out file in the first email, I have uploaded > > > another > > > > >>>> out file by mistake. The rest of the files are correct in the > first > > > mail. > > > > >>>> > > > > >>>> Regards > > > > >>>> Shamim Haque > > > > >>>> Senior Research Fellow (SRF) > > > > >>>> Department of Physics > > > > >>>> IISER Bhopal > > > > >>>> > > > > >>>> ? > > > > >>>> > > > > >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt < > sbrandt at cct.lsu.edu> > > > > >>>> wrote: > > > > >>>> > > > > >>>>> I notice from the output that your compiler claims "limits.h" > is > > > > >>>>> missing. Possibly there's something wrong with your icc > setup? > > > Maybe you > > > > >>>>> should try using gcc / gfortran instead. > > > > >>>>> > > > > >>>>> --Steve > > > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: > > > > >>>>> > > > > >>>>> Dear Frank, > > > > >>>>> > > > > >>>>> I added the alias pattern for the computing nodes and now ETK > can > > > > >>>>> detect the cluster (checked by asking "whoami") during the > batch > > > queuing. > > > > >>>>> I'll get in touch with the admins to include 'patch'. > > > > >>>>> > > > > >>>>> However, the problem still persists, having assured that the > > > correct > > > > >>>>> machine file and option list are being used during the > compilation. > > > > >>>>> > > > > >>>>> Regards > > > > >>>>> Shamim Haque > > > > >>>>> Senior Research Fellow (SRF) > > > > >>>>> Department of Physics > > > > >>>>> IISER Bhopal > > > > >>>>> > > > > >>>>> ? > > > > >>>>> > > > > >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < > > > > >>>>> frank.loeffler at uni-jena.de> wrote: > > > > >>>>> > > > > >>>>>> Hi Shamim > > > > >>>>>> > > > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque > 1910511 > > > wrote: > > > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. > The > > > > >>>>>> >compilation > > > > >>>>>> >stops at a very initial step and gives out the error: > > > > >>>>>> > > > > > >>>>>> >*checking whether the Fortran compiler (gfortran ) > works... > > > > >>>>>> yeschecking > > > > >>>>>> >whether the Fortran compiler (gfortran ) is a > > > cross-compiler... > > > > >>>>>> nochecking > > > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) > for > > > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C > preprocessor... > > > > >>>>>> cppchecking > > > > >>>>>> >for ANSI C header files... nochecking for C99 features... > > > > >>>>>> yeschecking for > > > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding > > > > >>>>>> -D_XOPEN_SOURCE to > > > > >>>>>> >CPPFLAGS.* > > > > >>>>>> > > > > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does > not > > > help. > > > > >>>>>> This > > > > >>>>>> >error is consistent if we set up using Intel Compiler (2020 > or > > > > >>>>>> 2019), or > > > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, > > > machine > > > > >>>>>> script, > > > > >>>>>> >and option lists for both cases (Intel and gcc) for any > > > reference. > > > > >>>>>> > > > > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. > So > > > we are > > > > >>>>>> >queuing a job script, which upon execution, enters the > Cactus > > > > >>>>>> directory, > > > > >>>>>> >does "setup-silent", and then executes the build command. > Is > > > this > > > > >>>>>> the right > > > > >>>>>> >way to compile ETK using the batch script? Or should we do > > > something > > > > >>>>>> >different? I have attached the shell script (compile.sh) > used > > > for > > > > >>>>>> sbatch > > > > >>>>>> >queue for reference. > > > > >>>>>> > > > > >>>>>> I might be wrong, but setup-silent will not use your machine > file > > > > >>>>>> which > > > > >>>>>> contains all the compiler flags, but will setup something > "from > > > > >>>>>> scratch" > > > > >>>>>> instead. According to the logs, this will be, e.g., in > > > > >>>>>> > > > > >>>>>> > > > > >>>>>> > > > > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini > > > > > >>>>>> > > > > >>>>>> My guess would be that this misses the compiler flags > necessary to > > > > >>>>>> have > > > > >>>>>> M_PI defined. The best way to get this working might be to let > > > > >>>>>> simfactory also detect the cluster configuration on the > compute > > > nodes > > > > >>>>>> (where you compile), such that setup-silent is not needed, but > > > > >>>>>> instead > > > > >>>>>> the correct cluster configuration is found and used > > > automatically. In > > > > >>>>>> order to do that, look at examples of 'aliaspattern' in the > > > > >>>>>> mdb/machines > > > > >>>>>> directory. An alternative would be to tell simfactory > specifically > > > > >>>>>> that > > > > >>>>>> you want to use your machine configuration file. > > > > >>>>>> > > > > >>>>>> As a side-note: I noticed the command 'patch' is missing > too. > > > This is > > > > >>>>>> a > > > > >>>>>> tool so common that it should be installed everywhere. Your > admin > > > is > > > > >>>>>> probably the best person to ask for advise here. It should > not be > > > too > > > > >>>>>> hard to install yourself, but that should not be necessary > either, > > > > >>>>>> especially when you are told to compile on compute nodes. > > > > >>>>>> > > > > >>>>>> Frank > > > > >>>>>> > > > > >>>>>> > > > > >>>>> _______________________________________________ > > > > >>>>> Users mailing listUsers at einsteintoolkit.orghttp:// > > > lists.einsteintoolkit.org/mailman/listinfo/users > > > > >>>>> > > > > >>>>> _______________________________________________ > > > > >>>>> Users mailing list > > > > >>>>> Users at einsteintoolkit.org > > > > >>>>> > > > > https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$ > > > > > >>>>> > > > > >>>> > > > > > > > > > Yours, > > > Roland > > > > > > -- > > > My email is as private as my paper mail. I therefore support encrypting > > > and signing email messages. Get my PGP key from > https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$ > . > > > > > -- > My email is as private as my paper mail. I therefore support encrypting > and signing email messages. Get my PGP key from http://pgp.mit.edu . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yrzsma at rit.edu Mon May 22 10:48:53 2023 From: yrzsma at rit.edu (Yosef Zlochower) Date: Mon, 22 May 2023 15:48:53 +0000 Subject: [Users] 2023 North American Einstein Toolkit School and Workshop (registration deadline approaching) Message-ID: Please note that the deadline to request partial travel support for the 2023 North American Einstein Toolkit School and Workshop is Thursday, June 1. The deadline for registration is June 17 The 2023 North American Einstein Toolkit School and Workshop will be held at the Rochester Institute of Technology on July 17 through July 21. This will be a hybrid conference with talks and participants both in-person and over zoom. The Einstein Toolkit is a community-driven software platform of core computational tools to advance and support research in relativistic astrophysics and gravitational physics. The conference consist of a mixture of tutorials for new users and talks about the latest developments both in the toolkit and the larger scientific community. A preliminary schedule and links to the registration page can be found at https://compact-binaries.org/content/events/2023-07-17/north-american-einstein-toolkit-school-and-workshop Registration is now open and remain open until June 17, 2023. As part of the registration process, potential attendees can apply for partial travel support. In order to be eligible, applications must be received prior to June 1. Notification of partial travel support will be made by June 8. From sbrandt at cct.lsu.edu Tue May 23 11:38:28 2023 From: sbrandt at cct.lsu.edu (Steven R. Brandt) Date: Tue, 23 May 2023 11:38:28 -0500 Subject: [Users] Thorn setup taking too much time in cluster In-Reply-To: References: <5e5208b8-c440-685a-ffd3-66cd03c3630a@cct.lsu.edu> Message-ID: Sorry that no one has replied to you in a while. Are you still experiencing this difficulty? --Steve On 4/4/2023 3:08 AM, Shamim Haque 1910511 wrote: > Dear Steven, > > I assure you that I submitted the simulation for the first time only. > I used "sim create-submit" to submit the simulation, which would not > submit the job if the same name was executed earlier. > > Secondly, I found this same message appearing in the output files from > debug queue (1 node, with GRHydro) and high memory node (3 nodes, with > IllinoisGRMHD), here the simulation ran successfully. I have attached > the output files for reference. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Tue, Apr 4, 2023 at 12:35?AM Steven R. Brandt > wrote: > > I see this error message in your output: > > ? -> [0m No HDF5 checkpoint files with basefilename > 'checkpoint.chkpt' and file extension '.h5' found in recovery > directory 'nsns_toy1.2_DDME2BPS_quark_1.2vs1.6M_40km_g25' > > I suspect you did a "sim submit" for a job, got a failure, and did > a second "sim submit" without purging. That immediately triggered > the error. Then, for some reason, MPI didn't shut down cleanly and > the processes hung doing nothing until they used up the walltime. > > --Steve > > On 4/2/2023 5:16 AM, Shamim Haque 1910511 wrote: >> Hello, >> >> I am trying to run BNSM using IllinoisGRMHD on HPC Kanad at IISER >> Bhopal. While I have tested the parfile to be running fine on >> debug queue (1 node) and high memory queue (3 nodes), I am unable >> to run the simulation in a queue with 9 nodes (144 cores). >> >> The output file suggests that the setup of listed thorns is not >> complete within 24 hours, which is the max walltime for this queue. >> >> Is there a way to sort out this?issue? I have attached the >> parfile and outfile for reference. >> >> Regards >> Shamim Haque >> Senior Research Fellow (SRF) >> Department of Physics >> IISER Bhopal >> ? >> >> _______________________________________________ >> Users mailing list >> Users at einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/users > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shamims at iiserb.ac.in Tue May 23 13:43:14 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Wed, 24 May 2023 00:13:14 +0530 Subject: [Users] Thorn setup taking too much time in cluster In-Reply-To: References: <5e5208b8-c440-685a-ffd3-66cd03c3630a@cct.lsu.edu> Message-ID: Dear Steve, Thank you for your reply. I tried the same simulation with a finer grid, and the simulation started working fine, even though very slow (looks like due to slow inter-node communication), but it did work out. I could see a few iterations towards the final couple of hours from the wall time. Turns out, a simulation with GRhydro, in such cases (where the grid needs to be finer), would end with an error saying, "*the grid structure inconsistent. Impossible to continue*". On the other hand, a simulation with IllinoisGRMHD stops abruptly during the thorn setup (somewhere around the SpaceMask and AHFinderDirect setup). Later I tried to see if I can pace up the simulation, but looks like the inter-node communication is very slow in the HPC, which may be an inherent problem with the HPC since it is a very old one. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Tue, May 23, 2023 at 10:08?PM Steven R. Brandt wrote: > Sorry that no one has replied to you in a while. Are you still > experiencing this difficulty? > > --Steve > On 4/4/2023 3:08 AM, Shamim Haque 1910511 wrote: > > Dear Steven, > > I assure you that I submitted the simulation for the first time only. I > used "sim create-submit" to submit the simulation, which would not submit > the job if the same name was executed earlier. > > Secondly, I found this same message appearing in the output files from > debug queue (1 node, with GRHydro) and high memory node (3 nodes, with > IllinoisGRMHD), here the simulation ran successfully. I have attached the > output files for reference. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Tue, Apr 4, 2023 at 12:35?AM Steven R. Brandt > wrote: > >> I see this error message in your output: >> >> -> [0m No HDF5 checkpoint files with basefilename 'checkpoint.chkpt' >> and file extension '.h5' found in recovery directory >> 'nsns_toy1.2_DDME2BPS_quark_1.2vs1.6M_40km_g25' >> >> I suspect you did a "sim submit" for a job, got a failure, and did a >> second "sim submit" without purging. That immediately triggered the error. >> Then, for some reason, MPI didn't shut down cleanly and the processes hung >> doing nothing until they used up the walltime. >> >> --Steve >> On 4/2/2023 5:16 AM, Shamim Haque 1910511 wrote: >> >> Hello, >> >> I am trying to run BNSM using IllinoisGRMHD on HPC Kanad at IISER Bhopal. >> While I have tested the parfile to be running fine on debug queue (1 node) >> and high memory queue (3 nodes), I am unable to run the simulation in a >> queue with 9 nodes (144 cores). >> >> The output file suggests that the setup of listed thorns is not complete >> within 24 hours, which is the max walltime for this queue. >> >> Is there a way to sort out this issue? I have attached the parfile and >> outfile for reference. >> >> Regards >> Shamim Haque >> Senior Research Fellow (SRF) >> Department of Physics >> IISER Bhopal >> ? >> >> _______________________________________________ >> Users mailing listUsers at einsteintoolkit.orghttp://lists.einsteintoolkit.org/mailman/listinfo/users >> >> _______________________________________________ >> Users mailing list >> Users at einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From scupp1 at my.apsu.edu Wed May 24 10:58:36 2023 From: scupp1 at my.apsu.edu (Cupp, Samuel D.) Date: Wed, 24 May 2023 15:58:36 +0000 Subject: [Users] New Einstein Toolkit Release (Schwarzschild) Message-ID: Release Announcement Click here to read the announcement in HTML (with hyperlinks): https://einsteintoolkit.org/about/releases/ET_2023_05_announcement.html We are pleased to announce the twenty-sixth release (code name "Karl Schwarzschild") of the Einstein Toolkit, an open-source, community-developed software infrastructure for relativistic astrophysics. The major changes in this release include: * kuibit 1.4.0, which, in addition to bug fixes, improves support for working with horizon data, timer data, and higher rank objects (See release notes for more details). Two new arrangements and thorns have been added: * The FUKA reader for numerical relativity initial data * TwoPunctures_BBHSF for binary black hole with scalar fields initial data New capabilities for existing codes: * Baikal and BaikalVacuum have been updated to have READ/WRITE declarations for automated ghost zone synchronization. Several variable groups (such as RHS variables) are also no longer included in checkpoint/restart operations. * particle_tracerET can now output the particles' four-velocity (contravariant and covariant); added support for binary output format; removed limit on the number of tracer particles In addition, bug fixes accumulated since the previous release in November 2022 have been included. The Einstein Toolkit is a collection of software components and tools for simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community, including code to compute initial data parameters, the spacetime evolution codes Baikal, lean_public, and McLachlan, analysis codes to compute horizon characteristics and gravitational waves, the Carpet AMR infrastructure, and the relativistic magneto-hydrodynamics codes GRHydro and IllinoisGRMHD. Data analysis and post-processing is handled by the kuibit library. The Einstein Toolkit also contains a 1D self-force code. For parts of the toolkit, the Cactus Framework is used as the underlying computational infrastructure, providing large-scale parallelization, general computational components, and a model for collaborative, portable code development. The Einstein Toolkit uses a distributed software model, and its different modules are developed, distributed, and supported either by the core team of Einstein Toolkit Maintainers or by individual groups. Where modules are provided by external groups, the Einstein Toolkit Maintainers provide quality control for modules for inclusion in the toolkit and help coordinate support. The Einstein Toolkit Maintainers currently involve staff and faculty from five different institutions and host weekly meetings that are open for anyone to join. Guiding principles for the design and implementation of the toolkit include: open, community-driven software development; well thought-out and stable interfaces; separation of physics software from computational science infrastructure; provision of complete working production code; training and education for a new generation of researchers. For more information about using or contributing to the Einstein Toolkit, or to join the Einstein Toolkit Consortium, please visit our web pages at http://einsteintoolkit.org, or contact the users mailing list users at einsteintoolkit.org. The Einstein Toolkit is primarily supported by NSF 2004157/2004044/2004311/2004879/2003893 (Enabling fundamental research in the era of multi-messenger astrophysics). The Einstein Toolkit contains about 350 regression test cases. On a large portion of the tested machines, almost all of these tests pass, using both MPI and OpenMP parallelization. Deprecated functionality There are no features marked as deprecated in this release, to be removed in the next release. Contributors Among the many contributors to the Einstein Toolkit and to this release in particular, important contributions to new components were made by the following authors: * Cheng-Hsin Cheng * Gabriele Bozzola * Leonardo Werneck * Ludwig Jens Papenfort * Samuel Cupp * Samuel Tootle How to upgrade from Kowalevski Release (ET_2022_11) To upgrade from the previous release, use GetComponents with the new thornlist to check out the new version. See the Download page (http://einsteintoolkit.org/download.html) on the Einstein Toolkit website for download instructions. The SelfForce-1D code uses a single git repository; thus, using git pull; git checkout ET_2023_05 will update the code. To install Kuibit, do the following: pip install --user -U kuibit==1.4.0 Machine notes Supported (tested) machines include: * Debian, Ubuntu, Fedora, Mint, OpenSUSE, and macOS X installations with dependencies installed as prescribed in the official installation instructions * Deep Bayou * Delta * Expanse * Frontera * Golub * Queen Bee 2 * Queen Bee 3 * Stampede 2 * Summit * Sunrise * SuperMIC * SuperMUC * ThornyFlat Note for individual machines: * TACC machines: defs.local.ini needs to have `sourcebasedir = $WORK` and `basedir = $SCRATCH/simulations` configured for this machine. You need to determine $WORK and $SCRATCH by logging in to the machine. * SuperMUC-NG: defs.local.ini needs to have `sourcebasedir = $HOME` and `basedir = $SCRATCH/simulations` configured for this machine. You need to determine $HOME and $SCRATCH by logging in to the machine. All repositories participating in this release carry a branch ET_2023_05 marking this release. These release branches will be updated if severe errors are found. The "Karl Schwarzschild" Release Team on behalf of the Einstein Toolkit Consortium (2023-05-24) * Leonardo Werneck * Samuel Cupp * Beyhan Karakas * Bing-Jyun Tsao * Cheng-Hsin Cheng * Jake Doherty * Konrad Topolski * Peter Diener * Roland Haas * Steven R. Brandt * Terrence Pierre Jacques * Thiago Assumpcao * Zachariah Etienne May 24, 2023 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hwitek at illinois.edu Thu May 25 04:38:00 2023 From: hwitek at illinois.edu (Helvi Witek) Date: Thu, 25 May 2023 10:38:00 +0100 Subject: [Users] New Einstein Toolkit Release (Schwarzschild) In-Reply-To: References: Message-ID: <694467c6-4ed1-2589-3dae-1165683154bb@illinois.edu> Dear Sam, Leo, thank you for spearheading the latest release of the Einstein Toolkit. This is important work for this community, and we very much appreciate it. We noticed that Giuseppe Ficarra (in cc) is not listed as contributor nor in the release team. Giuseppe is a co-author of the new Einstein Toolkit thorn "TwoPunctures_BBHSF." As per best scientific practices to credit scientific work, I would ask you to please add him as contributor and member of the release team on the Einstein Toolkit website and in the release notes. Best wishes, Helvi --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 --------------------------------------------- On 5/24/23 10:58 AM, Cupp, Samuel D. wrote: > Release Announcement > > Click here to read the announcement in HTML (with hyperlinks): > https://einsteintoolkit.org/about/releases/ET_2023_05_announcement.html > > > We are pleased to announce the twenty-sixth release (code name "Karl > Schwarzschild") of the Einstein Toolkit, an open-source, > community-developed software infrastructure for relativistic > astrophysics. The major changes in this release include: > > ?* kuibit 1.4.0, which, in addition to bug fixes, improves support > ? ?for working with horizon data, timer data, and higher rank objects > ? ?(See release notes for more details). > > Two new arrangements and thorns have been added: > > ?* The FUKA reader for numerical relativity initial data > ?* TwoPunctures_BBHSF for binary black hole with scalar fields > ? ?initial data > > New capabilities for existing codes: > > ?* Baikal and BaikalVacuum have been updated to have READ/WRITE > ? ?declarations for automated ghost zone synchronization. Several > ? ?variable groups (such as RHS variables) are also no longer > ? ?included in checkpoint/restart operations. > ?* particle_tracerET can now output the particles' four-velocity > ? ?(contravariant and covariant); added support for binary output > ? ?format; removed limit on the number of tracer particles > > In addition, bug fixes accumulated since the previous release in > November 2022 have been included. > > The Einstein Toolkit is a collection of software components and tools > for simulating and analyzing general relativistic astrophysical systems > that builds on numerous software efforts in the numerical relativity > community, including code to compute initial data parameters, the > spacetime evolution codes Baikal, lean_public, and McLachlan, analysis > codes to compute horizon characteristics and gravitational waves, the > Carpet AMR infrastructure, and the relativistic magneto-hydrodynamics > codes GRHydro and IllinoisGRMHD. Data analysis and post-processing is > handled by the kuibit library. The Einstein Toolkit also contains a 1D > self-force code. For parts of the toolkit, the Cactus Framework is used > as the underlying computational infrastructure, providing large-scale > parallelization, general computational components, and a model for > collaborative, portable code development. > > The Einstein Toolkit uses a distributed software model, and its > different modules are developed, distributed, and supported either by > the core team of Einstein Toolkit Maintainers or by individual groups. > Where modules are provided by external groups, the Einstein Toolkit > Maintainers provide quality control for modules for inclusion in the > toolkit and help coordinate support. The Einstein Toolkit Maintainers > currently involve staff and faculty from five different institutions and > host weekly meetings that are open for anyone to join. > > Guiding principles for the design and implementation of the toolkit > include: open, community-driven software development; well thought-out > and stable interfaces; separation of physics software from computational > science infrastructure; provision of complete working production code; > training and education for a new generation of researchers. > > For more information about using or contributing to the Einstein > Toolkit, or to join the Einstein Toolkit Consortium, please visit our > web pages at http://einsteintoolkit.org > , > or contact the users mailing > list users at einsteintoolkit.org. > > The Einstein Toolkit is primarily supported by NSF > 2004157/2004044/2004311/2004879/2003893 (Enabling fundamental research > in the era of multi-messenger astrophysics). > > The Einstein Toolkit contains about 350 regression test cases. On a > large portion of the tested machines, almost all of these tests pass, > using both MPI and OpenMP parallelization. > > Deprecated functionality > There are no features marked as deprecated in this release, to be > removed in the next release. > > Contributors > > Among the many contributors to the Einstein Toolkit and to this release > in particular, important contributions to new components were made by > the following authors: > > ?* Cheng-Hsin Cheng > ?* Gabriele Bozzola > ?* Leonardo Werneck > ?* Ludwig Jens Papenfort > ?* Samuel Cupp > ?* Samuel Tootle > > How to upgrade from Kowalevski Release (ET_2022_11) > > To upgrade from the previous release, use GetComponents with the new > thornlist to check out the new version. > > See the Download page (http://einsteintoolkit.org/download.html > ) > on the > Einstein Toolkit website for download instructions. > > The SelfForce-1D code uses a single git repository; thus, using > > git pull; git checkout ET_2023_05 > > will update the code. > > To install Kuibit, do the following: > > pip install --user -U kuibit==1.4.0 > > Machine notes > > Supported (tested) machines include: > > ?* Debian, Ubuntu, Fedora, Mint, OpenSUSE, and macOS X installations > ? ?with dependencies installed as prescribed in the official > ? ?installation instructions > ?* Deep Bayou > ?* Delta > ?* Expanse > ?* Frontera > ?* Golub > ?* Queen Bee 2 > ?* Queen Bee 3 > ?* Stampede 2 > ?* Summit > ?* Sunrise > ?* SuperMIC > ?* SuperMUC > ?* ThornyFlat > > Note for individual machines: > > ?* TACC machines: defs.local.ini needs to have `sourcebasedir = > ? ?$WORK` and `basedir = $SCRATCH/simulations` configured for this > ? ?machine. You need to determine $WORK and $SCRATCH by logging in to > ? ?the machine. > ?* SuperMUC-NG: defs.local.ini needs to have `sourcebasedir = $HOME` > ? ?and `basedir = $SCRATCH/simulations` configured for this machine. > ? ?You need to determine $HOME and $SCRATCH by logging in to the > ? ?machine. > > All repositories participating in this release carry a branch ET_2023_05 > marking this release. These release branches will be updated if severe > errors are found. > > The "Karl Schwarzschild" Release Team on behalf of the Einstein Toolkit > Consortium (2023-05-24) > > ?* Leonardo Werneck > ?* Samuel Cupp > ?* Beyhan Karakas > ?* Bing-Jyun Tsao > ?* Cheng-Hsin Cheng > ?* Jake Doherty > ?* Konrad Topolski > ?* Peter Diener > ?* Roland Haas > ?* Steven R. Brandt > ?* Terrence Pierre Jacques > ?* Thiago Assumpcao > ?* Zachariah Etienne > > May 24, 2023 > > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!5TkgZVyFsTZLkHtnyQibOcaEiP_lpMBil1TEXu_lpC-s4X2ZSwNUBCVriyx9oJIOvgS2lbgBsqHl6sx7VIBJ$ -------------- next part -------------- An HTML attachment was scrubbed... URL: From scupp1 at my.apsu.edu Thu May 25 09:37:30 2023 From: scupp1 at my.apsu.edu (Cupp, Samuel D.) Date: Thu, 25 May 2023 14:37:30 +0000 Subject: [Users] Meeting minutes for 2023-05-25 Message-ID: Present: Sam, Keith, Yosef, Peter, Roland, Zach Chair: Peter Notetaker: Sam * ET_2023_05 Release is out! Peter: Gallery example now has multiple resolutions. Should we include all the data? Will increase the amount of data being stored. Roland: We could just add the data specifically for the new plot and parameter files. Peter: I've already added the parfiles and can add the new data. * SPECv8 Roland: They've asked us for the exact version number of the code they are using. As far as we know, the ball is still in their court for moving forward with this. * Tickets Sam: I still need to close the tickets associated with the release, which I'll do today. Roland: Since we have just released a new version, now is the time to start considering more serious changes to code. One change is removing the compile flags from the linker stage. This is because for compiling with CUDA the linker stage shouldn't be assuming that it is the c++ compiler. This is sufficient to compile CarpetX, but it remains to be seen whether this change will be sufficient for external libraries. Zach: What is the plan for including CarpetX? Is it still coming soon? Roland: The idea is to have it added in the November release, but this will require quite a bit of work to get CarpetX ready for a release, both with code cleanup and testing compilation on different systems. Sam: I know some of the thorns need to be renamed to allow for smooth integration with the rest of the toolkit. Hopefully this will happen sooner rather than later. Peter: Had a conversation with Zach about Ticket #963 but hasn't had a chance to look at McLachlan again since that call. Zach: I found a different version of the 'third' change which has even better results than the original. I'll share that soon. Roland: We can merge Ticket #2731 (checking for incomplete perl install). A fix is also proposed for Ticket #2526 (incorrect read/writes generated by Kranc). Ian doesn't have time to review this, so Roland will try to track down the person who added the READ/WRITE declarations to Kranc. Next week the chair is Zach and the minute taker is Roland. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbrandt at cct.lsu.edu Thu May 25 10:12:18 2023 From: sbrandt at cct.lsu.edu (Steven R. Brandt) Date: Thu, 25 May 2023 10:12:18 -0500 Subject: [Users] New Einstein Toolkit Release (Schwarzschild) In-Reply-To: <694467c6-4ed1-2589-3dae-1165683154bb@illinois.edu> References: <694467c6-4ed1-2589-3dae-1165683154bb@illinois.edu> Message-ID: <50791e52-444c-8ccd-353f-59ef18c67e03@cct.lsu.edu> Yes, thank you both so much. The community is grateful for all you have done. --Steve On 5/25/2023 4:38 AM, Helvi Witek wrote: > > Dear Sam, Leo, > > thank you for spearheading the latest release of the Einstein Toolkit. > This is important work for this community, and we very much appreciate it. > > > We noticed that Giuseppe Ficarra (in cc) is not listed as contributor > nor in the release team. > Giuseppe is a co-author of the new Einstein Toolkit thorn > "TwoPunctures_BBHSF." > > > As per best scientific practices to credit scientific work, I would > ask you to please add him as contributor and member of the release > team on the Einstein Toolkit website and in the release notes. > > > Best wishes, > > Helvi > > --------------------------------------------- > Dr. Helvi Witek > Assistant Professor > Department of Physics > University of Illinois at Urbana-Champaign > > 247 Loomis Lab > 1110 W Green St > Urbana, IL 61801 > --------------------------------------------- > On 5/24/23 10:58 AM, Cupp, Samuel D. wrote: >> Release Announcement >> >> Click here to read the announcement in HTML (with hyperlinks): >> https://einsteintoolkit.org/about/releases/ET_2023_05_announcement.html >> >> >> We are pleased to announce the twenty-sixth release (code name "Karl >> Schwarzschild") of the Einstein Toolkit, an open-source, >> community-developed software infrastructure for relativistic >> astrophysics. The major changes in this release include: >> >> ?* kuibit 1.4.0, which, in addition to bug fixes, improves support >> ? ?for working with horizon data, timer data, and higher rank objects >> ? ?(See release notes for more details). >> >> Two new arrangements and thorns have been added: >> >> ?* The FUKA reader for numerical relativity initial data >> ?* TwoPunctures_BBHSF for binary black hole with scalar fields >> ? ?initial data >> >> New capabilities for existing codes: >> >> ?* Baikal and BaikalVacuum have been updated to have READ/WRITE >> ? ?declarations for automated ghost zone synchronization. Several >> ? ?variable groups (such as RHS variables) are also no longer >> ? ?included in checkpoint/restart operations. >> ?* particle_tracerET can now output the particles' four-velocity >> ? ?(contravariant and covariant); added support for binary output >> ? ?format; removed limit on the number of tracer particles >> >> In addition, bug fixes accumulated since the previous release in >> November 2022 have been included. >> >> The Einstein Toolkit is a collection of software components and tools >> for simulating and analyzing general relativistic astrophysical systems >> that builds on numerous software efforts in the numerical relativity >> community, including code to compute initial data parameters, the >> spacetime evolution codes Baikal, lean_public, and McLachlan, analysis >> codes to compute horizon characteristics and gravitational waves, the >> Carpet AMR infrastructure, and the relativistic magneto-hydrodynamics >> codes GRHydro and IllinoisGRMHD. Data analysis and post-processing is >> handled by the kuibit library. The Einstein Toolkit also contains a 1D >> self-force code. For parts of the toolkit, the Cactus Framework is used >> as the underlying computational infrastructure, providing large-scale >> parallelization, general computational components, and a model for >> collaborative, portable code development. >> >> The Einstein Toolkit uses a distributed software model, and its >> different modules are developed, distributed, and supported either by >> the core team of Einstein Toolkit Maintainers or by individual groups. >> Where modules are provided by external groups, the Einstein Toolkit >> Maintainers provide quality control for modules for inclusion in the >> toolkit and help coordinate support. The Einstein Toolkit Maintainers >> currently involve staff and faculty from five different institutions and >> host weekly meetings that are open for anyone to join. >> >> Guiding principles for the design and implementation of the toolkit >> include: open, community-driven software development; well thought-out >> and stable interfaces; separation of physics software from computational >> science infrastructure; provision of complete working production code; >> training and education for a new generation of researchers. >> >> For more information about using or contributing to the Einstein >> Toolkit, or to join the Einstein Toolkit Consortium, please visit our >> web pages at http://einsteintoolkit.org >> , >> or contact the users mailing >> list users at einsteintoolkit.org. >> >> The Einstein Toolkit is primarily supported by NSF >> 2004157/2004044/2004311/2004879/2003893 (Enabling fundamental research >> in the era of multi-messenger astrophysics). >> >> The Einstein Toolkit contains about 350 regression test cases. On a >> large portion of the tested machines, almost all of these tests pass, >> using both MPI and OpenMP parallelization. >> >> Deprecated functionality >> There are no features marked as deprecated in this release, to be >> removed in the next release. >> >> Contributors >> >> Among the many contributors to the Einstein Toolkit and to this release >> in particular, important contributions to new components were made by >> the following authors: >> >> ?* Cheng-Hsin Cheng >> ?* Gabriele Bozzola >> ?* Leonardo Werneck >> ?* Ludwig Jens Papenfort >> ?* Samuel Cupp >> ?* Samuel Tootle >> >> How to upgrade from Kowalevski Release (ET_2022_11) >> >> To upgrade from the previous release, use GetComponents with the new >> thornlist to check out the new version. >> >> See the Download page (http://einsteintoolkit.org/download.html >> ) >> on the >> Einstein Toolkit website for download instructions. >> >> The SelfForce-1D code uses a single git repository; thus, using >> >> git pull; git checkout ET_2023_05 >> >> will update the code. >> >> To install Kuibit, do the following: >> >> pip install --user -U kuibit==1.4.0 >> >> Machine notes >> >> Supported (tested) machines include: >> >> ?* Debian, Ubuntu, Fedora, Mint, OpenSUSE, and macOS X installations >> ? ?with dependencies installed as prescribed in the official >> ? ?installation instructions >> ?* Deep Bayou >> ?* Delta >> ?* Expanse >> ?* Frontera >> ?* Golub >> ?* Queen Bee 2 >> ?* Queen Bee 3 >> ?* Stampede 2 >> ?* Summit >> ?* Sunrise >> ?* SuperMIC >> ?* SuperMUC >> ?* ThornyFlat >> >> Note for individual machines: >> >> ?* TACC machines: defs.local.ini needs to have `sourcebasedir = >> ? ?$WORK` and `basedir = $SCRATCH/simulations` configured for this >> ? ?machine. You need to determine $WORK and $SCRATCH by logging in to >> ? ?the machine. >> ?* SuperMUC-NG: defs.local.ini needs to have `sourcebasedir = $HOME` >> ? ?and `basedir = $SCRATCH/simulations` configured for this machine. >> ? ?You need to determine $HOME and $SCRATCH by logging in to the >> ? ?machine. >> >> All repositories participating in this release carry a branch ET_2023_05 >> marking this release. These release branches will be updated if severe >> errors are found. >> >> The "Karl Schwarzschild" Release Team on behalf of the Einstein Toolkit >> Consortium (2023-05-24) >> >> ?* Leonardo Werneck >> ?* Samuel Cupp >> ?* Beyhan Karakas >> ?* Bing-Jyun Tsao >> ?* Cheng-Hsin Cheng >> ?* Jake Doherty >> ?* Konrad Topolski >> ?* Peter Diener >> ?* Roland Haas >> ?* Steven R. Brandt >> ?* Terrence Pierre Jacques >> ?* Thiago Assumpcao >> ?* Zachariah Etienne >> >> May 24, 2023 >> >> _______________________________________________ >> Users mailing list >> Users at einsteintoolkit.org >> https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!5TkgZVyFsTZLkHtnyQibOcaEiP_lpMBil1TEXu_lpC-s4X2ZSwNUBCVriyx9oJIOvgS2lbgBsqHl6sx7VIBJ$ > > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -------------- next part -------------- An HTML attachment was scrubbed... URL: From shamims at iiserb.ac.in Wed May 31 16:26:38 2023 From: shamims at iiserb.ac.in (Shamim Haque 1910511) Date: Thu, 1 Jun 2023 02:56:38 +0530 Subject: [Users] Compilation Error in cluster ParamGanga In-Reply-To: References: <74397676-cd6a-551e-ef18-b5df77edfc71@cct.lsu.edu> <4449ed77-ac78-8774-896b-f86737ea9bf0@cct.lsu.edu> <20230511135018.1d31cfb1@ekohaes8> <20230518090147.4248b227@ekohaes8> Message-ID: Hello All, I have made little progress on compiling ETK on this cluster, as the admins allowed me to compile ETK on the login node. I am finding new errors and am unable to debug the issue. I am trying to configure ETK using Intel19, and the error says the following: */home/shamims.iiserb/ET_debug/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc(160): error: more than one instance of overloaded function "CarpetMask::isnan" matches the argument list: function "isnan(double)" function "std::isnan(double)" argument types are: (CCTK_REAL8) assert(not isnan(phi)); ^compilation aborted for /home/shamims.iiserb/ET_debug/Cactus/configs/sim/build/CarpetMask/mask_surface.cc (code 2)make[3]: *** [mask_surface.cc.o] Error 2make[2]: *** [make.checked] Error 2make[1]: *** [/home/shamims.iiserb/ET_debug/Cactus/configs/sim/lib/libthorn_CarpetMask.a] Error 2make: *** [sim] Error 2* I have attached the machinefile, optionlist, config log and full output file for reference. I configured the scripts using the available example optionlist and machinefile for supermuc_ng and stampede2. Please let me know if more info is required, and thanks in advance for your help. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ? On Fri, May 19, 2023 at 2:32?PM Shamim Haque 1910511 wrote: > Hello Roland, > > Thank you for the reply. Yes, I am trying to compile ETK in the computing > node via sbatch queue. I am in touch with the system admin to resolve > the issue with the compilers. > > Regards > Shamim Haque > Senior Research Fellow (SRF) > Department of Physics > IISER Bhopal > > ? > > On Thu, May 18, 2023 at 7:32?PM Roland Haas wrote: > >> Hello Shamin, >> >> A missing math.h would point to a faulty compiler installation. Since >> you are trying to compile (are you?) ona compute node in a running job, >> my guess would be that the cluster admins are not providing compilers >> on the compute nodes but only on the login nodes. >> >> This would be something to contact your cluster's help desk about. >> >> Yours, >> Roland >> >> > Hello Roland, >> > >> > I did try that fix; the error remains the same. Actually, we landed on >> an >> > even more primitive problem, where Steve suggested a basic test, that >> is to >> > compile the following code: >> > >> > >> > >> > >> > >> > >> > >> > *#include #include int main() { printf("%f\n", >> > M_PI); return 0;}* >> > >> > This program compiles just fine in the login node but gives out the >> > following error while compiling it via jobscript submission in the >> sbatch >> > queue: >> > >> > prog.cpp:1:18: fatal error: math.h: No such file or directory >> > #include >> > ^ >> > compilation terminated. >> > >> > ----OR----- >> > >> > >> /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: >> > fatal error: features.h: No such file or directory >> > 39 | #include >> > | ^~~~~~~~~~~~ >> > compilation terminated. >> > >> > I have reported this problem to the HPC admin and await their response. >> > >> > Regards >> > Shamim Haque >> > Senior Research Fellow (SRF) >> > Department of Physics >> > IISER Bhopal >> > >> > ? >> > >> > On Fri, May 12, 2023 at 12:20?AM Roland Haas >> wrote: >> > >> > > Hello all, >> > > >> > > Since the error is a missing M_PI and the configure script already >> > > gives a suggested fix: >> > > >> > > Try adding -D_XOPEN_SOURCE to CPPFLAGS. >> > > >> > > have you tried adding: >> > > >> > > CPPFLAGS=-D_XOPEN_SOURCE >> > > >> > > to your option list file before compiling? >> > > >> > > Yours, >> > > Roland >> > > >> > > > Thanks Steve. I have raised complaint to the admin about this issue. >> > > > >> > > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt < >> sbrandt at cct.lsu.edu> >> > > wrote: >> > > > >> > > > > I would talk to the system administrators about that. There is >> > > definitely >> > > > > something wrong with your compiler install if you can't find >> math.h. >> > > > > >> > > > > --Steve >> > > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote: >> > > > > >> > > > > Dear Steve, >> > > > > >> > > > > I just rechecked the cpp program to output M_PI in the computing >> nodes, >> > > > > and that is not working right now, which was somehow working fine >> a few >> > > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, >> > > gnu8/8.3) >> > > > > available in the cluster. All report similar issue: >> > > > > >> > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory >> > > > > #include >> > > > > ^ >> > > > > compilation terminated. >> > > > > >> > > > > ----OR----- >> > > > > >> > > > > >> > > >> /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: >> >> > > > > fatal error: features.h: No such file or directory >> > > > > 39 | #include >> > > > > | ^~~~~~~~~~~~ >> > > > > compilation terminated. >> > > > > >> > > > > The cpp code seems to work fine in login node, as it gives out >> the >> > > value >> > > > > of pi upon execution. I am contacting the hpc admin to resolve >> this >> > > issue. >> > > > > >> > > > > I am attaching the test code (prog.cpp), the sbatch jobscript >> (prog.sh) >> > > > > and the output file (slurn-117473.out), if you would like to have >> a >> > > look at >> > > > > it. >> > > > > >> > > > > Please let me know if I should try something different to get >> this >> > > working. >> > > > > >> > > > > Regards >> > > > > Shamim Haque >> > > > > Senior Research Fellow (SRF) >> > > > > Department of Physics >> > > > > IISER Bhopal >> > > > > >> > > > > ? >> > > > > >> > > > > On Mon, May 8, 2023 at 7:25?PM Shamim Haque 1910511 < >> > > shamims at iiserb.ac.in> >> > > > > wrote: >> > > > > >> > > > >> Thanks Steve. I'll make the changes and try again. I'll let you >> know >> > > the >> > > > >> outcome. >> > > > >> >> > > > >> Regards >> > > > >> Shamim Haque >> > > > >> Senior Research Fellow (SRF) >> > > > >> Department of Physics >> > > > >> IISER Bhopal >> > > > >> >> > > > >> ? >> > > > >> >> > > > >> On Mon, May 8, 2023 at 7:21?PM Steven R. Brandt < >> sbrandt at cct.lsu.edu> >> > > > >> wrote: >> > > > >> >> > > > >>> That tends to make me think you aren't using the compiler you >> think >> > > > >>> you're using. You could put full paths in the .cfg files and >> > > recompile from >> > > > >>> scratch. >> > > > >>> >> > > > >>> i.e. >> > > > >>> >> > > > >>> CXX = /full/path/to/icc >> > > > >>> >> > > > >>> --Steve >> > > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote: >> > > > >>> >> > > > >>> Yes, this gives the value of Pi successfully, before starting >> the >> > > > >>> compilation: >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: >> paramganga3 >> > > Using >> > > > >>> configuration: sim Reconfiguring sim Writing configuration to: >> > > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList >> Cactus - >> > > > >>> version: 4.12.0 Reconfiguring sim. * >> > > > >>> *.* >> > > > >>> *.* >> > > > >>> *.* >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> >> > > > >>> *checking for M_PI... no configure: error: M_PI not defined. >> Try >> > > adding >> > > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config >> make: *** >> > > > >>> [sim-config] Error 2 * >> > > > >>> >> > > > >>> >> > > > >>> Shamim Haque >> > > > >>> Senior Research Fellow (SRF) >> > > > >>> Department of Physics >> > > > >>> IISER Bhopal >> > > > >>> >> > > > >>> ? >> > > > >>> >> > > > >>> On Thu, May 4, 2023 at 12:29?AM Steven Brandt < >> sbrandt at cct.lsu.edu> >> > > > >>> wrote: >> > > > >>> >> > > > >>>> So, sanity check, can you compile the following program >> outside of >> > > > >>>> Cactus? >> > > > >>>> >> > > > >>>> #include >> > > > >>>> #include >> > > > >>>> >> > > > >>>> int main() { >> > > > >>>> printf("%f\n", M_PI); >> > > > >>>> return 0; >> > > > >>>> } >> > > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote: >> > > > >>>> >> > > > >>>> Dear Steve, >> > > > >>>> >> > > > >>>> I tried gcc (10 and 11) as well and I am stuck with the >> following >> > > error: >> > > > >>>> *configure: error: M_PI not defined. Try adding >> -D_XOPEN_SOURCE to >> > > > >>>> CPPFLAGS.* >> > > > >>>> >> > > > >>>> This also happened for Intel (2020 and 2019). I have attached >> both >> > > the >> > > > >>>> output files here. >> > > > >>>> >> > > > >>>> Please ignore the out file in the first email, I have >> uploaded >> > > another >> > > > >>>> out file by mistake. The rest of the files are correct in the >> first >> > > mail. >> > > > >>>> >> > > > >>>> Regards >> > > > >>>> Shamim Haque >> > > > >>>> Senior Research Fellow (SRF) >> > > > >>>> Department of Physics >> > > > >>>> IISER Bhopal >> > > > >>>> >> > > > >>>> ? >> > > > >>>> >> > > > >>>> On Wed, May 3, 2023 at 8:04?PM Steven Brandt < >> sbrandt at cct.lsu.edu> >> > > > >>>> wrote: >> > > > >>>> >> > > > >>>>> I notice from the output that your compiler claims "limits.h" >> is >> > > > >>>>> missing. Possibly there's something wrong with your icc >> setup? >> > > Maybe you >> > > > >>>>> should try using gcc / gfortran instead. >> > > > >>>>> >> > > > >>>>> --Steve >> > > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote: >> > > > >>>>> >> > > > >>>>> Dear Frank, >> > > > >>>>> >> > > > >>>>> I added the alias pattern for the computing nodes and now ETK >> can >> > > > >>>>> detect the cluster (checked by asking "whoami") during the >> batch >> > > queuing. >> > > > >>>>> I'll get in touch with the admins to include 'patch'. >> > > > >>>>> >> > > > >>>>> However, the problem still persists, having assured that the >> > > correct >> > > > >>>>> machine file and option list are being used during the >> compilation. >> > > > >>>>> >> > > > >>>>> Regards >> > > > >>>>> Shamim Haque >> > > > >>>>> Senior Research Fellow (SRF) >> > > > >>>>> Department of Physics >> > > > >>>>> IISER Bhopal >> > > > >>>>> >> > > > >>>>> ? >> > > > >>>>> >> > > > >>>>> On Wed, May 3, 2023 at 3:49?PM Frank Loeffler < >> > > > >>>>> frank.loeffler at uni-jena.de> wrote: >> > > > >>>>> >> > > > >>>>>> Hi Shamim >> > > > >>>>>> >> > > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque >> 1910511 >> > > wrote: >> > > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. >> The >> > > > >>>>>> >compilation >> > > > >>>>>> >stops at a very initial step and gives out the error: >> > > > >>>>>> > >> > > > >>>>>> >*checking whether the Fortran compiler (gfortran ) >> works... >> > > > >>>>>> yeschecking >> > > > >>>>>> >whether the Fortran compiler (gfortran ) is a >> > > cross-compiler... >> > > > >>>>>> nochecking >> > > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) >> for >> > > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C >> preprocessor... >> > > > >>>>>> cppchecking >> > > > >>>>>> >for ANSI C header files... nochecking for C99 features... >> > > > >>>>>> yeschecking for >> > > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding >> > > > >>>>>> -D_XOPEN_SOURCE to >> > > > >>>>>> >CPPFLAGS.* >> > > > >>>>>> > >> > > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does >> not >> > > help. >> > > > >>>>>> This >> > > > >>>>>> >error is consistent if we set up using Intel Compiler (2020 >> or >> > > > >>>>>> 2019), or >> > > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, >> > > machine >> > > > >>>>>> script, >> > > > >>>>>> >and option lists for both cases (Intel and gcc) for any >> > > reference. >> > > > >>>>>> > >> > > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. >> So >> > > we are >> > > > >>>>>> >queuing a job script, which upon execution, enters the >> Cactus >> > > > >>>>>> directory, >> > > > >>>>>> >does "setup-silent", and then executes the build command. >> Is >> > > this >> > > > >>>>>> the right >> > > > >>>>>> >way to compile ETK using the batch script? Or should we do >> > > something >> > > > >>>>>> >different? I have attached the shell script (compile.sh) >> used >> > > for >> > > > >>>>>> sbatch >> > > > >>>>>> >queue for reference. >> > > > >>>>>> >> > > > >>>>>> I might be wrong, but setup-silent will not use your machine >> file >> > > > >>>>>> which >> > > > >>>>>> contains all the compiler flags, but will setup something >> "from >> > > > >>>>>> scratch" >> > > > >>>>>> instead. According to the logs, this will be, e.g., in >> > > > >>>>>> >> > > > >>>>>> >> > > > >>>>>> >> > > >> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini >> >> > > > >>>>>> >> > > > >>>>>> My guess would be that this misses the compiler flags >> necessary to >> > > > >>>>>> have >> > > > >>>>>> M_PI defined. The best way to get this working might be to >> let >> > > > >>>>>> simfactory also detect the cluster configuration on the >> compute >> > > nodes >> > > > >>>>>> (where you compile), such that setup-silent is not needed, >> but >> > > > >>>>>> instead >> > > > >>>>>> the correct cluster configuration is found and used >> > > automatically. In >> > > > >>>>>> order to do that, look at examples of 'aliaspattern' in the >> > > > >>>>>> mdb/machines >> > > > >>>>>> directory. An alternative would be to tell simfactory >> specifically >> > > > >>>>>> that >> > > > >>>>>> you want to use your machine configuration file. >> > > > >>>>>> >> > > > >>>>>> As a side-note: I noticed the command 'patch' is missing >> too. >> > > This is >> > > > >>>>>> a >> > > > >>>>>> tool so common that it should be installed everywhere. Your >> admin >> > > is >> > > > >>>>>> probably the best person to ask for advise here. It should >> not be >> > > too >> > > > >>>>>> hard to install yourself, but that should not be necessary >> either, >> > > > >>>>>> especially when you are told to compile on compute nodes. >> > > > >>>>>> >> > > > >>>>>> Frank >> > > > >>>>>> >> > > > >>>>>> >> > > > >>>>> _______________________________________________ >> > > > >>>>> Users mailing listUsers at einsteintoolkit.orghttp:// >> > > lists.einsteintoolkit.org/mailman/listinfo/users >> > > > >>>>> >> > > > >>>>> _______________________________________________ >> > > > >>>>> Users mailing list >> > > > >>>>> Users at einsteintoolkit.org >> > > > >>>>> >> > > >> https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$ >> >> > > > >>>>> >> > > > >>>> >> > > >> > > >> > > Yours, >> > > Roland >> > > >> > > -- >> > > My email is as private as my paper mail. I therefore support >> encrypting >> > > and signing email messages. Get my PGP key from >> https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$ >> . >> > > >> >> -- >> My email is as private as my paper mail. I therefore support encrypting >> and signing email messages. Get my PGP key from http://pgp.mit.edu . >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: paramganga.ini Type: application/octet-stream Size: 3232 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: paramganga.cfg Type: application/octet-stream Size: 2539 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: config.log Type: text/x-log Size: 52839 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: intel19_compile.out Type: application/octet-stream Size: 244180 bytes Desc: not available URL: From vik at arizona.edu Mon May 1 18:47:01 2023 From: vik at arizona.edu (Vikram Manikantan) Date: Mon, 01 May 2023 23:47:01 -0000 Subject: [Users] Warning: No boundary conditions registered for variables in group LEANBSSNMOL Message-ID: Hi, I am a new user of Einstein Toolkit, using the latest version (ET_2022_11). I have recently encountered issues with the Lean thorn that lead to warnings concerning the registered boundary conditions. I filed a bug report here . And possibly related to issue #2651 . To reproduce the issue, just add the line Cactus::presync_mode = "mixed-warn" to the *Lean_inspiral_d06_mres.par *file in repos/lean_public/par/. The warnings I get look like: -> No boundary conditions registered for variables in group LEANBSSNMOL::GAMMAT. The unregistered variable(s) is(are) LEANBSSNMOL::gammatx, LEANBSSNMOL::gammaty, LEANBSSNMOL::gammatz. There are hundreds of lines like this. Is this a concern? I am happy to produce any extra information needed. Thanks! Best, Vikram -------------- next part -------------- An HTML attachment was scrubbed... URL: From jrativa at unal.edu.co Wed May 3 18:55:34 2023 From: jrativa at unal.edu.co (Jose Luis Rativa Medina) Date: Wed, 03 May 2023 23:55:34 -0000 Subject: [Users] PROBLEM RUNNING GW150914 Message-ID: Hi, I'm trying to run the GW150914 simulation on my MSI GF63 9sc but the parameter file contains python code and I don't know how to run it. Thanks -- *Jos? Luis Rativa Medina* *Estudiante ing. sistemas y computaci?n* *Universidad Nacional de Colombia* -- *Aviso legal:*?El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos s?lo para el uso del destinatario al cual van enviados. La reproducci?n, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, inf?rmenos y elim?nelo de su correo. Los Datos Personales ser?n tratados conforme a la Ley 1581 de 2012 y a nuestra Pol?tica de Datos Personales que podr? consultar en la p?gina web? www.unal.edu.co .*?*Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electr?nico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entender? como personales y de ninguna manera son avaladas por la Universidad. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nils.vu at black-holes.org Sun May 7 13:15:43 2023 From: nils.vu at black-holes.org (Nils Vu) Date: Sun, 07 May 2023 18:15:43 -0000 Subject: [Users] Today (Mon): NR community call at 9am Pacific / noon NYC / 5pm London / 6pm Berlin Message-ID: <3A1F9A37-7ED8-423E-AB5A-CF1BBC51BA31@black-holes.org> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: zoom.ico Type: image/x-icon Size: 4286 bytes Desc: not available URL: From brookluo34 at hotmail.com Wed May 10 13:22:52 2023 From: brookluo34 at hotmail.com (Yufeng Luo) Date: Wed, 10 May 2023 18:22:52 -0000 Subject: [Users] Compiling failure on Mac with Apple Silicon M2 chip Message-ID: <025E2D5E-E8BD-458E-AFFA-142CCF2E559D@hotmail.com> Hello, I was trying to compile ET_2022_11 on a M2 Macbook Pro machine, but I got an error. I attached my compilation output below. It seems that the general configuration script correctly recognized my machine with a aarch64 (line 50) processor, but when compiling openSSL thorn (line 2933) the compilation script incorrectly marked the machine as i686. My understanding is that apple silicon (M1) is now supported in the newest version of ET (2022 11). Since M1 and M2 have the same ARMv8 architecture, I was wondering if there is an error in openSSL thorn? Thank you. Best, Yufeng -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: compile_output.txt URL: From crh at panix.com Thu May 25 05:14:44 2023 From: crh at panix.com (crh at panix.com) Date: Thu, 25 May 2023 10:14:44 -0000 Subject: [Users] HELP with error installing ET_2023_05 Message-ID: <068f01d98ef1$b4bedc90$1e3c95b0$@panix.com> Dear Users of The Einstein Toolkit: I am installing the recent version of The Einstein Toolkit, ET_2023_05. When I run the following command git clone -b ET_2023_05 https://bitbucket.org/peterdiener/selfforce-1d.git SelfForce-1D I get the following error message: Cloning into 'SelfForce-1D'... fatal: Remote branch ET_2023_05 not found in upstream origin Would anyone know a solution to this error? Thank you. Best Regards, Charles R. Hurley Home e-mail: crh at panix.com -------------- next part -------------- An HTML attachment was scrubbed... URL: