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] >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>>>> >>>>
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