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 rhaas@illinois.edu 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 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
ᐧ
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
ᐧ
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
ᐧ
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://
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Yours, Roland
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