<div dir="ltr"><div class="gmail_default" style="color:#000000"><div class="gmail_default">Hello All,</div><div class="gmail_default"><br></div><div class="gmail_default">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:</div><div class="gmail_default"><i><font color="#a64d79"><br></font></i></div><div class="gmail_default"><i><font color="#a64d79">/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:<br> function "isnan(double)"<br> function "std::isnan(double)"<br> argument types are: (CCTK_REAL8)<br> assert(not isnan(phi));<br> ^<br>compilation aborted for /home/shamims.iiserb/ET_debug/Cactus/configs/sim/build/CarpetMask/mask_surface.cc (code 2)<br>make[3]: *** [mask_surface.cc.o] Error 2<br>make[2]: *** [make.checked] Error 2<br>make[1]: *** [/home/shamims.iiserb/ET_debug/Cactus/configs/sim/lib/libthorn_CarpetMask.a] Error 2<br>make: *** [sim] Error 2</font></i></div><div class="gmail_default"><br></div><div class="gmail_default">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.</div><div class="gmail_default"><br></div><div class="gmail_default">Regards</div></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font color="#666666">Shamim Haque</font></div><div dir="ltr"><font color="#666666">Senior Research Fellow (SRF)<br></font><div><font color="#666666">Department of Physics</font></div><div><font color="#666666">IISER Bhopal</font></div></div></div></div></div></div></div></div></div></div><br></div><div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width:0px;max-height:0px;overflow:hidden" src="https://mailfoogae.appspot.com/t?sender=ac2hhbWltc0BpaXNlcmIuYWMuaW4%3D&type=zerocontent&guid=ab8f90ea-d9a9-4374-b217-c67afc647a3e"><font color="#ffffff" size="1">ᐧ</font></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 19, 2023 at 2:32 PM Shamim Haque 1910511 <<a href="mailto:shamims@iiserb.ac.in">shamims@iiserb.ac.in</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="color:rgb(0,0,0)">Hello Roland,</div><div class="gmail_default" style="color:rgb(0,0,0)"><br></div><div class="gmail_default" style="color:rgb(0,0,0)">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.</div><div class="gmail_default" style="color:rgb(0,0,0)"><br></div><div class="gmail_default" style="color:rgb(0,0,0)">Regards</div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font color="#666666">Shamim Haque</font></div><div dir="ltr"><font color="#666666">Senior Research Fellow (SRF)<br></font><div><font color="#666666">Department of Physics</font></div><div><font color="#666666">IISER Bhopal</font></div></div></div></div></div></div></div></div></div></div><br></div><div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width: 0px; max-height: 0px; overflow: hidden;" src="https://mailfoogae.appspot.com/t?sender=ac2hhbWltc0BpaXNlcmIuYWMuaW4%3D&type=zerocontent&guid=f7097955-5202-4778-bb09-c5e26f7abb64"><font color="#ffffff" size="1">ᐧ</font></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 18, 2023 at 7:32 PM Roland Haas <<a href="mailto:rhaas@illinois.edu" target="_blank">rhaas@illinois.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello Shamin,<br>
<br>
A missing math.h would point to a faulty compiler installation. Since<br>
you are trying to compile (are you?) ona compute node in a running job,<br>
my guess would be that the cluster admins are not providing compilers<br>
on the compute nodes but only on the login nodes.<br>
<br>
This would be something to contact your cluster's help desk about.<br>
<br>
Yours,<br>
Roland<br>
<br>
> Hello Roland,<br>
> <br>
> I did try that fix; the error remains the same. Actually, we landed on an<br>
> even more primitive problem, where Steve suggested a basic test, that is to<br>
> compile the following code:<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> *#include <math.h>#include <stdio.h>int main() { printf("%f\n",<br>
> M_PI); return 0;}*<br>
> <br>
> This program compiles just fine in the login node but gives out the<br>
> following error while compiling it via jobscript submission in the sbatch<br>
> queue:<br>
> <br>
> prog.cpp:1:18: fatal error: math.h: No such file or directory<br>
> #include <math.h><br>
> ^<br>
> compilation terminated.<br>
> <br>
> ----OR-----<br>
> <br>
> /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10:<br>
> fatal error: features.h: No such file or directory<br>
> 39 | #include <features.h><br>
> | ^~~~~~~~~~~~<br>
> compilation terminated.<br>
> <br>
> I have reported this problem to the HPC admin and await their response.<br>
> <br>
> Regards<br>
> Shamim Haque<br>
> Senior Research Fellow (SRF)<br>
> Department of Physics<br>
> IISER Bhopal<br>
> <br>
> ᐧ<br>
> <br>
> On Fri, May 12, 2023 at 12:20 AM Roland Haas <<a href="mailto:rhaas@illinois.edu" target="_blank">rhaas@illinois.edu</a>> wrote:<br>
> <br>
> > Hello all,<br>
> ><br>
> > Since the error is a missing M_PI and the configure script already<br>
> > gives a suggested fix:<br>
> ><br>
> > Try adding -D_XOPEN_SOURCE to CPPFLAGS.<br>
> ><br>
> > have you tried adding:<br>
> ><br>
> > CPPFLAGS=-D_XOPEN_SOURCE<br>
> ><br>
> > to your option list file before compiling?<br>
> ><br>
> > Yours,<br>
> > Roland<br>
> > <br>
> > > Thanks Steve. I have raised complaint to the admin about this issue.<br>
> > ><br>
> > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>> <br>
> > wrote: <br>
> > > <br>
> > > > I would talk to the system administrators about that. There is <br>
> > definitely <br>
> > > > something wrong with your compiler install if you can't find math.h.<br>
> > > ><br>
> > > > --Steve<br>
> > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote:<br>
> > > ><br>
> > > > Dear Steve,<br>
> > > ><br>
> > > > I just rechecked the cpp program to output M_PI in the computing nodes,<br>
> > > > and that is not working right now, which was somehow working fine a few<br>
> > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, <br>
> > gnu8/8.3) <br>
> > > > available in the cluster. All report similar issue:<br>
> > > ><br>
> > > > prog.cpp:1:18: fatal error: math.h: No such file or directory<br>
> > > > #include <math.h><br>
> > > > ^<br>
> > > > compilation terminated.<br>
> > > ><br>
> > > > ----OR-----<br>
> > > ><br>
> > > > <br>
> > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: <br>
> > > > fatal error: features.h: No such file or directory<br>
> > > > 39 | #include <features.h><br>
> > > > | ^~~~~~~~~~~~<br>
> > > > compilation terminated.<br>
> > > ><br>
> > > > The cpp code seems to work fine in login node, as it gives out the <br>
> > value <br>
> > > > of pi upon execution. I am contacting the hpc admin to resolve this <br>
> > issue. <br>
> > > ><br>
> > > > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh)<br>
> > > > and the output file (slurn-117473.out), if you would like to have a <br>
> > look at <br>
> > > > it.<br>
> > > ><br>
> > > > Please let me know if I should try something different to get this <br>
> > working. <br>
> > > ><br>
> > > > Regards<br>
> > > > Shamim Haque<br>
> > > > Senior Research Fellow (SRF)<br>
> > > > Department of Physics<br>
> > > > IISER Bhopal<br>
> > > ><br>
> > > > ᐧ<br>
> > > ><br>
> > > > On Mon, May 8, 2023 at 7:25 PM Shamim Haque 1910511 < <br>
> > <a href="mailto:shamims@iiserb.ac.in" target="_blank">shamims@iiserb.ac.in</a>> <br>
> > > > wrote:<br>
> > > > <br>
> > > >> Thanks Steve. I'll make the changes and try again. I'll let you know <br>
> > the <br>
> > > >> outcome.<br>
> > > >><br>
> > > >> Regards<br>
> > > >> Shamim Haque<br>
> > > >> Senior Research Fellow (SRF)<br>
> > > >> Department of Physics<br>
> > > >> IISER Bhopal<br>
> > > >><br>
> > > >> ᐧ<br>
> > > >><br>
> > > >> On Mon, May 8, 2023 at 7:21 PM Steven R. Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> > > >> wrote:<br>
> > > >> <br>
> > > >>> That tends to make me think you aren't using the compiler you think<br>
> > > >>> you're using. You could put full paths in the .cfg files and <br>
> > recompile from <br>
> > > >>> scratch.<br>
> > > >>><br>
> > > >>> i.e.<br>
> > > >>><br>
> > > >>> CXX = /full/path/to/icc<br>
> > > >>><br>
> > > >>> --Steve<br>
> > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote:<br>
> > > >>><br>
> > > >>> Yes, this gives the value of Pi successfully, before starting the<br>
> > > >>> compilation:<br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 <br>
> > Using <br>
> > > >>> configuration: sim Reconfiguring sim Writing configuration to:<br>
> > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus -<br>
> > > >>> version: 4.12.0 Reconfiguring sim. *<br>
> > > >>> *.*<br>
> > > >>> *.*<br>
> > > >>> *.*<br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>><br>
> > > >>> *checking for M_PI... no configure: error: M_PI not defined. Try <br>
> > adding <br>
> > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: ***<br>
> > > >>> [sim-config] Error 2 *<br>
> > > >>><br>
> > > >>><br>
> > > >>> Shamim Haque<br>
> > > >>> Senior Research Fellow (SRF)<br>
> > > >>> Department of Physics<br>
> > > >>> IISER Bhopal<br>
> > > >>><br>
> > > >>> ᐧ<br>
> > > >>><br>
> > > >>> On Thu, May 4, 2023 at 12:29 AM Steven Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> > > >>> wrote:<br>
> > > >>> <br>
> > > >>>> So, sanity check, can you compile the following program outside of<br>
> > > >>>> Cactus?<br>
> > > >>>><br>
> > > >>>> #include <math.h><br>
> > > >>>> #include <stdio.h><br>
> > > >>>><br>
> > > >>>> int main() {<br>
> > > >>>> printf("%f\n", M_PI);<br>
> > > >>>> return 0;<br>
> > > >>>> }<br>
> > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote:<br>
> > > >>>><br>
> > > >>>> Dear Steve,<br>
> > > >>>><br>
> > > >>>> I tried gcc (10 and 11) as well and I am stuck with the following <br>
> > error: <br>
> > > >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to<br>
> > > >>>> CPPFLAGS.*<br>
> > > >>>><br>
> > > >>>> This also happened for Intel (2020 and 2019). I have attached both <br>
> > the <br>
> > > >>>> output files here.<br>
> > > >>>><br>
> > > >>>> Please ignore the out file in the first email, I have uploaded <br>
> > another <br>
> > > >>>> out file by mistake. The rest of the files are correct in the first <br>
> > mail. <br>
> > > >>>><br>
> > > >>>> Regards<br>
> > > >>>> Shamim Haque<br>
> > > >>>> Senior Research Fellow (SRF)<br>
> > > >>>> Department of Physics<br>
> > > >>>> IISER Bhopal<br>
> > > >>>><br>
> > > >>>> ᐧ<br>
> > > >>>><br>
> > > >>>> On Wed, May 3, 2023 at 8:04 PM Steven Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> > > >>>> wrote:<br>
> > > >>>> <br>
> > > >>>>> I notice from the output that your compiler claims "limits.h" is<br>
> > > >>>>> missing. Possibly there's something wrong with your icc setup? <br>
> > Maybe you <br>
> > > >>>>> should try using gcc / gfortran instead.<br>
> > > >>>>><br>
> > > >>>>> --Steve<br>
> > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote:<br>
> > > >>>>><br>
> > > >>>>> Dear Frank,<br>
> > > >>>>><br>
> > > >>>>> I added the alias pattern for the computing nodes and now ETK can<br>
> > > >>>>> detect the cluster (checked by asking "whoami") during the batch <br>
> > queuing. <br>
> > > >>>>> I'll get in touch with the admins to include 'patch'.<br>
> > > >>>>><br>
> > > >>>>> However, the problem still persists, having assured that the <br>
> > correct <br>
> > > >>>>> machine file and option list are being used during the compilation.<br>
> > > >>>>><br>
> > > >>>>> Regards<br>
> > > >>>>> Shamim Haque<br>
> > > >>>>> Senior Research Fellow (SRF)<br>
> > > >>>>> Department of Physics<br>
> > > >>>>> IISER Bhopal<br>
> > > >>>>><br>
> > > >>>>> ᐧ<br>
> > > >>>>><br>
> > > >>>>> On Wed, May 3, 2023 at 3:49 PM Frank Loeffler <<br>
> > > >>>>> <a href="mailto:frank.loeffler@uni-jena.de" target="_blank">frank.loeffler@uni-jena.de</a>> wrote:<br>
> > > >>>>> <br>
> > > >>>>>> Hi Shamim<br>
> > > >>>>>><br>
> > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 <br>
> > wrote: <br>
> > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee. The<br>
> > > >>>>>> >compilation<br>
> > > >>>>>> >stops at a very initial step and gives out the error:<br>
> > > >>>>>> ><br>
> > > >>>>>> >*checking whether the Fortran compiler (gfortran ) works... <br>
> > > >>>>>> yeschecking <br>
> > > >>>>>> >whether the Fortran compiler (gfortran ) is a <br>
> > cross-compiler... <br>
> > > >>>>>> nochecking <br>
> > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for<br>
> > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... <br>
> > > >>>>>> cppchecking <br>
> > > >>>>>> >for ANSI C header files... nochecking for C99 features... <br>
> > > >>>>>> yeschecking for <br>
> > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding <br>
> > > >>>>>> -D_XOPEN_SOURCE to <br>
> > > >>>>>> >CPPFLAGS.*<br>
> > > >>>>>> ><br>
> > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not <br>
> > help. <br>
> > > >>>>>> This <br>
> > > >>>>>> >error is consistent if we set up using Intel Compiler (2020 or <br>
> > > >>>>>> 2019), or <br>
> > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file, <br>
> > machine <br>
> > > >>>>>> script, <br>
> > > >>>>>> >and option lists for both cases (Intel and gcc) for any <br>
> > reference. <br>
> > > >>>>>> ><br>
> > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes. So <br>
> > we are <br>
> > > >>>>>> >queuing a job script, which upon execution, enters the Cactus <br>
> > > >>>>>> directory, <br>
> > > >>>>>> >does "setup-silent", and then executes the build command. Is <br>
> > this <br>
> > > >>>>>> the right <br>
> > > >>>>>> >way to compile ETK using the batch script? Or should we do <br>
> > something <br>
> > > >>>>>> >different? I have attached the shell script (compile.sh) used <br>
> > for <br>
> > > >>>>>> sbatch <br>
> > > >>>>>> >queue for reference. <br>
> > > >>>>>><br>
> > > >>>>>> I might be wrong, but setup-silent will not use your machine file<br>
> > > >>>>>> which<br>
> > > >>>>>> contains all the compiler flags, but will setup something "from<br>
> > > >>>>>> scratch"<br>
> > > >>>>>> instead. According to the logs, this will be, e.g., in<br>
> > > >>>>>><br>
> > > >>>>>><br>
> > > >>>>>> <br>
> > /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini <br>
> > > >>>>>><br>
> > > >>>>>> My guess would be that this misses the compiler flags necessary to<br>
> > > >>>>>> have<br>
> > > >>>>>> M_PI defined. The best way to get this working might be to let<br>
> > > >>>>>> simfactory also detect the cluster configuration on the compute <br>
> > nodes <br>
> > > >>>>>> (where you compile), such that setup-silent is not needed, but<br>
> > > >>>>>> instead<br>
> > > >>>>>> the correct cluster configuration is found and used <br>
> > automatically. In <br>
> > > >>>>>> order to do that, look at examples of 'aliaspattern' in the<br>
> > > >>>>>> mdb/machines<br>
> > > >>>>>> directory. An alternative would be to tell simfactory specifically<br>
> > > >>>>>> that<br>
> > > >>>>>> you want to use your machine configuration file.<br>
> > > >>>>>><br>
> > > >>>>>> As a side-note: I noticed the command 'patch' is missing too. <br>
> > This is <br>
> > > >>>>>> a<br>
> > > >>>>>> tool so common that it should be installed everywhere. Your admin <br>
> > is <br>
> > > >>>>>> probably the best person to ask for advise here. It should not be <br>
> > too <br>
> > > >>>>>> hard to install yourself, but that should not be necessary either,<br>
> > > >>>>>> especially when you are told to compile on compute nodes.<br>
> > > >>>>>><br>
> > > >>>>>> Frank<br>
> > > >>>>>><br>
> > > >>>>>> <br>
> > > >>>>> _______________________________________________<br>
> > > >>>>> Users mailing listUsers@einsteintoolkit.orghttp:// <br>
> > <a href="http://lists.einsteintoolkit.org/mailman/listinfo/users" rel="noreferrer" target="_blank">lists.einsteintoolkit.org/mailman/listinfo/users</a> <br>
> > > >>>>><br>
> > > >>>>> _______________________________________________<br>
> > > >>>>> Users mailing list<br>
> > > >>>>> <a href="mailto:Users@einsteintoolkit.org" target="_blank">Users@einsteintoolkit.org</a><br>
> > > >>>>> <br>
> > <a href="https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$</a> <br>
> > > >>>>> <br>
> > > >>>> <br>
> ><br>
> ><br>
> > Yours,<br>
> > Roland<br>
> ><br>
> > --<br>
> > My email is as private as my paper mail. I therefore support encrypting<br>
> > and signing email messages. Get my PGP key from <a href="https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$</a> .<br>
> > <br>
<br>
-- <br>
My email is as private as my paper mail. I therefore support encrypting<br>
and signing email messages. Get my PGP key from <a href="http://pgp.mit.edu" rel="noreferrer" target="_blank">http://pgp.mit.edu</a> .<br>
</blockquote></div>
</blockquote></div>