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<p>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.</p>
<p>--Steve<br>
</p>
<div class="moz-cite-prefix">On 5/3/2023 8:20 AM, Shamim Haque
1910511 wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAHrQTHXcKpDN3TUKjO=QzxzL43iovEnp+O2k3BkTL5AaV_XH=Q@mail.gmail.com">
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<div class="gmail_default" style="color:#000000">Dear Frank,</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">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'.</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">However, the
problem still persists, having assured that the correct
machine file and option list are being used during the
compilation.</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">Regards</div>
<div>
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<div dir="ltr"><font color="#666666">Shamim
Haque</font></div>
<div dir="ltr"><font color="#666666">Senior
Research Fellow (SRF)<br>
</font>
<div><font color="#666666">Department of
Physics</font></div>
<div><font color="#666666">IISER Bhopal</font></div>
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<div dir="ltr" class="gmail_attr">On Wed, May 3, 2023 at 3:49 PM
Frank Loeffler <<a href="mailto:frank.loeffler@uni-jena.de"
moz-do-not-send="true" class="moz-txt-link-freetext">frank.loeffler@uni-jena.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
Shamim<br>
<br>
On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511
wrote:<br>
>We are trying to compile ETK on ParamGanga at IIT Roorkee.
The <br>
>compilation<br>
>stops at a very initial step and gives out the error:<br>
><br>
>*checking whether the Fortran compiler (gfortran )
works... yeschecking<br>
>whether the Fortran compiler (gfortran ) is a
cross-compiler... nochecking<br>
>whether the Fortran compiler (gfortran ) supports TYPE(*)
for<br>
>CCTK_PointerTo... yeschecking how to run the C
preprocessor... cppchecking<br>
>for ANSI C header files... nochecking for C99 features...
yeschecking for<br>
>M_PI... noconfigure: error: M_PI not defined. Try adding
-D_XOPEN_SOURCE to<br>
>CPPFLAGS.*<br>
><br>
>We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does
not help. This<br>
>error is consistent if we set up using Intel Compiler
(2020 or 2019), or<br>
>gcc (11 or 10). I have attached the outfile, error file,
machine script,<br>
>and option lists for both cases (Intel and gcc) for any
reference.<br>
><br>
>Secondly, we are not allowed to compile ETK on login
nodes. So we are<br>
>queuing a job script, which upon execution, enters the
Cactus directory,<br>
>does "setup-silent", and then executes the build command.
Is this the right<br>
>way to compile ETK using the batch script? Or should we do
something<br>
>different? I have attached the shell script (compile.sh)
used for sbatch<br>
>queue for reference.<br>
<br>
I might be wrong, but setup-silent will not use your machine
file which <br>
contains all the compiler flags, but will setup something
"from scratch" <br>
instead. According to the logs, this will be, e.g., in<br>
<br>
/home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini<br>
<br>
My guess would be that this misses the compiler flags
necessary to have <br>
M_PI defined. The best way to get this working might be to let
<br>
simfactory also detect the cluster configuration on the
compute nodes <br>
(where you compile), such that setup-silent is not needed, but
instead <br>
the correct cluster configuration is found and used
automatically. In <br>
order to do that, look at examples of 'aliaspattern' in the
mdb/machines <br>
directory. An alternative would be to tell simfactory
specifically that <br>
you want to use your machine configuration file.<br>
<br>
As a side-note: I noticed the command 'patch' is missing too.
This is a <br>
tool so common that it should be installed everywhere. Your
admin is <br>
probably the best person to ask for advise here. It should not
be too <br>
hard to install yourself, but that should not be necessary
either, <br>
especially when you are told to compile on compute nodes.<br>
<br>
Frank<br>
<br>
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