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
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