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 ᐧ On Tue, Jun 6, 2023 at 6:56 PM Roland Haas <rh...@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 <rh...@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 < > > > sham...@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 <rh...@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 < > rh...@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 < > > > > >> sbra...@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 < > > > > >> > > sham...@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 < > > > > >> sbra...@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 < > > > > >> sbra...@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 < > > > > >> sbra...@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.loeff...@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@einsteintoolkit.orghttp:// > > > > >> > > lists.einsteintoolkit.org/mailman/listinfo/users > > > > >> > > > >>>>> > > > > >> > > > >>>>> _______________________________________________ > > > > >> > > > >>>>> Users mailing list > > > > >> > > > >>>>> Users@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 http://pgp.mit.edu . >
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