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@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
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On Mon, May 8, 2023 at 7:25 PM Shamim Haque 1910511 shamims@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@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
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On Thu, May 4, 2023 at 12:29 AM Steven Brandt sbrandt@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
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On Wed, May 3, 2023 at 8:04 PM Steven Brandt sbrandt@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@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
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Yours, Roland