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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > > > > 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 < > > > [email protected]> > > > > > 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 < > [email protected]> > > > > >> 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 < > [email protected]> > > > > >>> 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 < > [email protected]> > > > > >>>> 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 < > > > > >>>>> [email protected]> 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 [email protected]:// > > > lists.einsteintoolkit.org/mailman/listinfo/users > > > > >>>>> > > > > >>>>> _______________________________________________ > > > > >>>>> Users mailing list > > > > >>>>> [email protected] > > > > >>>>> > > > > 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 . >
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