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]http://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 http://pgp.mit.edu .
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