[Users] Compilation Error in cluster ParamGanga

Roland Haas rhaas at illinois.edu
Mon Jun 19 11:13:10 CDT 2023


Hello Shamim Haque,

Great. Glad that we could help you.

Yours,
Roland

> Dear Roland, Steve and Frank,
> 
> I am able to compile ETK properly with GNU compiler 8.3.0. The simulations
> are also running successfully.
> 
> For Intel, the licence issue was cleared after using -j1, but there are a
> few issues with other libraries, so I have stopped exploring this
> route right now, maybe I'll try it later.
> 
> Thank you for all the help.
> 
> Regards
> Shamim Haque
> Senior Research Fellow (SRF)
> Department of Physics
> IISER Bhopal
> 
>> 
> On Tue, Jun 6, 2023 at 6:56 PM Roland Haas <rhaas at illinois.edu> wrote:
> 
> > Hello Shamim Haque,
> >
> > "icpc unable to checkout FLEXlm license" is caused by the compiler
> > being unable to contact the license server. This is unrelated to the
> > C++ compilation issue really.
> >
> > To be sure:
> >
> > * the only thing you did was add
> >   "-gxx-name=/opt/ohpc/pub/compiler/gcc/8.3.0/bin/g++" was it? In
> >   particular you did not add / remove any "module load" commands (e.g.,
> >   added a module load gcc after an existing module load intel)? I am
> >   asking b/c module load gcc may unload the intel compiler module and
> >   unset the environment variable that the Intel compiler uses to
> >   determine how to contact the license server.
> >
> > * you may also try to compile with just "make -j1" or
> >   "simfactory/bin/sim build -j1" to use only a single compiler instance
> >   in case the number of compiler licenses available is limited or the
> >   license server overwhelmed by too many concurrent compilations (by
> >   you or other users of the cluster)
> >
> > The issue with fftw3 and using gcc is that fftw3 (you are using a
> > system provided fftw3? Either from a module or otherwise provided by
> > the admin) has been compiled with the Intel compiler and thus cannot be
> > used with the GNU compiler. You an set "FFTW_DIR = BUILD" to make the
> > Einstein Toolkit build a copy from scratch using an included tar file.
> > Not that this may be the case for other libraries as well. In
> > particular you usually need to ensure that the MPI library used was
> > compiled with the same compiler you use to compile the simulation code.
> >
> > Yours,
> > Roland
> >  
> > > Hello Roland,
> > >
> > > Thank you for the reply.
> > >
> > > I pointed -gxx-name to gcc/8.3.0, which resulted in an error related to  
> > the  
> > > "icpc unable to checkout FLEXlm license". I also tried to use a
> > > different intel compiler (and point -gxx-name to gcc/11.1.0) to check if
> > > the error can go away, but it remains the same. I communicated this to  
> > the  
> > > HPC admin and awaiting their response; please let me know if I should fix
> > > something in my configuration. I have attached the out file
> > > (intel_compile.out), config log (intel_config.log),
> > > and optionlist (intel.cfg) for reference.
> > >
> > > Meanwhile, I also attempted to configure ET with gcc/11.1.0, which  
> > resulted  
> > > in some issues regarding the FFTW3. I have contacted the admins regarding
> > > this, but please let me know if it is something to be fixed within the
> > > optionlist. I have attached the out file (gcc_compile.out), config log
> > > (gcc_config.log), and optionlist (gcc.cfg) for reference.
> > >
> > > The error in the output file says the following:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *Formaline:  is still running, e.g. the final link stage.)/usr/bin/ld:
> > > warning: libimf.so, needed by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so,
> > > not found (try using -rpath or -rpath-link)/usr/bin/ld: warning:
> > > libsvml.so, needed by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not  
> > found  
> > > (try using -rpath or -rpath-link)/usr/bin/ld: warning: libirng.so, needed
> > > by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not found (try using  
> > -rpath  
> > > or -rpath-link)/usr/bin/ld: warning: libintlc.so.5, needed by
> > > /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not found (try using -rpath  
> > or  
> > > -rpath-link)/usr/bin/ld: warning: libgfortran.so.3, needed by
> > > /lib/../lib64/liblapack.so, may conflict with
> > > libgfortran.so.5/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > > reference to
> > > `__intel_cpu_features_init_x'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:
> > > undefined reference to
> > > `__svml_sincos2'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > > reference to
> > > `_intel_fast_memset'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > > reference to
> > >  
> > `__intel_cpu_feature_indicator_x'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:  
> > > undefined reference to
> > > `_intel_fast_memmove'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:  
> > undefined  
> > > reference to `_intel_fast_memcpy'*
> > >
> > > Thanks in advance for all the help.
> > >
> > > Regards
> > > Shamim
> > >
> > > ᐧ
> > >
> > > On Fri, Jun 2, 2023 at 1:31 AM Roland Haas <rhaas at illinois.edu> wrote:
> > >  
> > > > Hello Shamim Haque,
> > > >
> > > > This most likely is caused by not having a full C++11 software stack
> > > > enabled.
> > > >
> > > > The Intel compiler always uses the C++ STL library of the GNU g++
> > > > compiler and must be matched up with a compatible g++ compiler's STL
> > > > to correctly support C++11.
> > > >
> > > > This ticket (the last of many, hopefully) contains details:
> > > >
> > > >
> > > >  
> > https://urldefense.com/v3/__https://bitbucket.org/einsteintoolkit/tickets/issues/2663/add-an-notice-about-minimum-intel-gcc__;!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlRGRwlyl$  
> > > >
> > > > Basically, the fix is to find a gcc compiler at least version 6 on your
> > > > cluster, then pass the option
> > > >
> > > > -gxx-name PATH-TO-GXX
> > > >
> > > > to icpc in the CXXFLAGS option list variable (see eg
> > > >
> > > >  
> > https://urldefense.com/v3/__https://bitbucket.org/simfactory/simfactory2/src/7e2592d264b1afe9ca2cb54bcab8dd9e4165cf98/mdb/optionlists/smic-openmpi.cfg?at=master*smic-openmpi.cfg-15:16__;Iw!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlSBbGTFf$  
> > > > ).
> > > >
> > > > If there is no gcc compiler version 6 or newer installed in the system,
> > > > you will have to contact the administrators and ask them about it.
> > > >
> > > > The demo code in the description of
> > > >  
> > https://urldefense.com/v3/__https://bitbucket.org/cactuscode/cactus/pull-requests/152__;!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlUmecdAQ$
> > may help  
> > > > demonstrate to the admins what the issue is.
> > > >
> > > > Yours,
> > > > Roland
> > > >  
> > > > > 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
> > > > >
> > > > > ᐧ
> > > > >
> > > > > On Fri, May 19, 2023 at 2:32 PM Shamim Haque 1910511 <
> > > > shamims at iiserb.ac.in>
> > > > > 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
> > > > > >
> > > > > > ᐧ
> > > > > >
> > > > > > On Thu, May 18, 2023 at 7:32 PM Roland Haas <rhaas at illinois.edu>  
> > > > 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 <math.h>#include <stdio.h>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 <math.h>
> > > > > >> >                   ^
> > > > > >> > 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 <features.h>
> > > > > >> >       |          ^~~~~~~~~~~~
> > > > > >> > 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
> > > > > >> >
> > > > > >> > ᐧ
> > > > > >> >
> > > > > >> > On Fri, May 12, 2023 at 12:20 AM Roland Haas <  
> > rhaas at illinois.edu>  
> > > > > >> 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 <math.h>
> > > > > >> > > > >                   ^
> > > > > >> > > > > 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 <features.h>
> > > > > >> > > > >       |          ^~~~~~~~~~~~
> > > > > >> > > > > 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
> > > > > >> > > > >
> > > > > >> > > > > ᐧ
> > > > > >> > > > >
> > > > > >> > > > > 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
> > > > > >> > > > >>
> > > > > >> > > > >> ᐧ
> > > > > >> > > > >>
> > > > > >> > > > >> 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
> > > > > >> > > > >>>
> > > > > >> > > > >>> ᐧ
> > > > > >> > > > >>>
> > > > > >> > > > >>> 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 <math.h>
> > > > > >> > > > >>>> #include <stdio.h>
> > > > > >> > > > >>>>
> > > > > >> > > > >>>> 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
> > > > > >> > > > >>>>
> > > > > >> > > > >>>> ᐧ
> > > > > >> > > > >>>>
> > > > > >> > > > >>>> 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
> > > > > >> > > > >>>>>
> > > > > >> > > > >>>>> ᐧ
> > > > > >> > > > >>>>>
> > > > > >> > > > >>>>> 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  
> > > >  
> > https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!9Rc70AgC5_rUJApjF6bdaoR4iJf6WXHxF1UsHWThqJwM8QxTwHKDWcVgn0kphw4Lmahcfk5a8gMIPSpV8TMD$  
> > > > .  
> > > > > >>  
> > > > > >  
> > > >
> > > >
> > > > --
> > > > 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!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlS57nxFF$
> > .  
> > > >  
> >
> >
> > 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!74UYivLDsgDyPF-Kn9OePqrK6mQFaU6DJIWuNHV41ASctcTTwQkuwK5QhQdt4fQakEt4WOp6BDVKkL7EO8fH$  .
> >  



-- 
My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from http://keys.gnupg.net.
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