[Users] Compilation Error in cluster ParamGanga
Roland Haas
rhaas at illinois.edu
Thu May 11 13:50:18 CDT 2023
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 http://pgp.mit.edu .
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 833 bytes
Desc: OpenPGP digital signature
URL: <http://lists.einsteintoolkit.org/pipermail/users/attachments/20230511/7dac61ba/attachment.sig>
More information about the Users
mailing list