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.loeff...@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
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