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<p>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.</p>
<p>--Steve<br>
</p>
<div class="moz-cite-prefix">On 5/11/2023 2:02 AM, Shamim Haque
1910511 wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAHrQTHX37Y3Vqf8dK5frZU=O0nMyfBV3-mpFuVwv36XKpoAPmA@mail.gmail.com">
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<div class="gmail_default" style="color:#000000">Dear Steve,</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">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:</div>
<div class="gmail_default" style=""><font color="#a64d79"><br>
</font></div>
<div class="gmail_default" style=""><font color="#a64d79">prog.cpp:1:18:
fatal error: math.h: No such file or directory<br>
#include <math.h><br>
^<br>
compilation terminated.</font><br>
</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">----OR-----</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<font color="#741b47">/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<br>
39 | #include <features.h><br>
| ^~~~~~~~~~~~<br>
</font>
<div class="gmail_default" style=""><font color="#741b47">compilation
terminated. </font></div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">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.<br>
</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">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. </div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style="color:#000000">Please let me
know if I should try something different to get this working.</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">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
<br>
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<div dir="ltr" class="gmail_attr">On Mon, May 8, 2023 at 7:25 PM
Shamim Haque 1910511 <<a href="mailto:shamims@iiserb.ac.in"
moz-do-not-send="true" class="moz-txt-link-freetext">shamims@iiserb.ac.in</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">
<div dir="ltr">
<div class="gmail_default" style="color:rgb(0,0,0)">Thanks
Steve. I'll make the changes and try again. I'll let you
know the outcome.</div>
<div class="gmail_default" style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default" style="color:rgb(0,0,0)">Regards</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 8, 2023 at
7:21 PM Steven R. Brandt <<a
href="mailto:sbrandt@cct.lsu.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">sbrandt@cct.lsu.edu</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">
<div>
<p>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.</p>
<p>i.e.</p>
<p>CXX = /full/path/to/icc<br>
</p>
<p>--Steve<br>
</p>
<div>On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default" style="color:rgb(0,0,0)">Yes,
this gives the value of Pi successfully, before
starting the compilation:</div>
<div class="gmail_default" style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"><i><font color="#741b47">/home/vkerni.iitr/sam/trial<br>
3.141593<br>
Current machine: paramganga3<br>
Using configuration: sim<br>
Reconfiguring sim<br>
Writing configuration to:
/home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList<br>
Cactus - version: 4.12.0<br>
Reconfiguring sim.<br>
</font></i></div>
<div class="gmail_default"><i><font color="#741b47">.</font></i></div>
<div class="gmail_default"><i><font color="#741b47">.</font></i></div>
<div class="gmail_default"><i><font color="#741b47">.</font></i></div>
<div class="gmail_default"><i><font color="#741b47">checking
for M_PI... no<br>
configure: error: M_PI not defined. Try adding
-D_XOPEN_SOURCE to CPPFLAGS.<br>
<br>
Error reconfiguring sim-config<br>
make: *** [sim-config] Error 2<br>
</font></i></div>
<div class="gmail_default" style="color:rgb(0,0,0)"><br>
</div>
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<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 4,
2023 at 12:29 AM Steven Brandt <<a
href="mailto:sbrandt@cct.lsu.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">sbrandt@cct.lsu.edu</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">
<div>
<p>So, sanity check, can you compile the
following program outside of Cactus?<br>
</p>
<p>#include <math.h><br>
#include <stdio.h><br>
<br>
int main() {<br>
printf("%f\n", M_PI);<br>
return 0;<br>
}</p>
<div>On 5/3/2023 1:50 PM, Shamim Haque 1910511
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default"
style="color:rgb(0,0,0)">Dear Steve,</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">I tried gcc (10
and 11) as well and I am stuck with the
following error:</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><i>configure:
error: M_PI not defined. Try adding
-D_XOPEN_SOURCE to CPPFLAGS.</i><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><i><br>
</i></div>
<div class="gmail_default"
style="color:rgb(0,0,0)">This also
happened for Intel (2020 and 2019). I
have attached both the output files here. </div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">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.</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">Regards</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed,
May 3, 2023 at 8:04 PM Steven Brandt <<a
href="mailto:sbrandt@cct.lsu.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">sbrandt@cct.lsu.edu</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">
<div>
<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>On 5/3/2023 8:20 AM, Shamim Haque
1910511 wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default"
style="color:rgb(0,0,0)">Dear
Frank,</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">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:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">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:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">Regards</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
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<br>
<div class="gmail_quote">
<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"
target="_blank"
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>
</blockquote>
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