<div dir="ltr"><div class="gmail_default" style="color:#000000">Hello Roland,</div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style="color:#000000">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:</div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style=""><i style=""><font color="#a64d79">#include <math.h><br style="">#include <stdio.h><br style="">int main() {<br style=""> printf("%f\n", M_PI);<br style=""> return 0;<br style="">}</font><br></i></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)"><br></span></div><div class="gmail_default" style=""><font color="#000000">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:</font></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)"> </span></div><div class="gmail_default" style="color:#000000"><div class="gmail_default" style="color:rgb(34,34,34)"><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"><br></div><div class="gmail_default">----OR-----</div><div class="gmail_default"><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="color:rgb(34,34,34)"><font color="#741b47">compilation terminated.</font></div></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)"><br></span></div><div class="gmail_default" style=""><font color="#000000">I have reported this problem to the HPC admin and await their response.</font></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)"><br></span></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)">Regards</span></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)">Shamim Haque</span></div><div class="gmail_default" style="color:#000000"><span style="color:rgb(102,102,102)">Senior Research Fellow (SRF)</span></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><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><div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width:0px;max-height:0px;overflow:hidden" src="https://mailfoogae.appspot.com/t?sender=ac2hhbWltc0BpaXNlcmIuYWMuaW4%3D&type=zerocontent&guid=176b1de1-d13e-4b28-b5ba-70c963a34180"><font color="#ffffff" size="1">ᐧ</font></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 12, 2023 at 12:20 AM Roland Haas <<a href="mailto:rhaas@illinois.edu">rhaas@illinois.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">Hello all,<br>
<br>
Since the error is a missing M_PI and the configure script already<br>
gives a suggested fix:<br>
<br>
Try adding -D_XOPEN_SOURCE to CPPFLAGS.<br>
<br>
have you tried adding:<br>
<br>
CPPFLAGS=-D_XOPEN_SOURCE<br>
<br>
to your option list file before compiling?<br>
<br>
Yours,<br>
Roland<br>
<br>
> Thanks Steve. I have raised complaint to the admin about this issue.<br>
> <br>
> On Thu, May 11, 2023, 11:18 PM Steven R. Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>> wrote:<br>
> <br>
> > I would talk to the system administrators about that. There is definitely<br>
> > something wrong with your compiler install if you can't find math.h.<br>
> ><br>
> > --Steve<br>
> > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote:<br>
> ><br>
> > Dear Steve,<br>
> ><br>
> > I just rechecked the cpp program to output M_PI in the computing nodes,<br>
> > and that is not working right now, which was somehow working fine a few<br>
> > days ago. I also tried different gcc versions (4.8, 10.2, 11.1, gnu8/8.3)<br>
> > available in the cluster. All report similar issue:<br>
> ><br>
> > prog.cpp:1:18: fatal error: math.h: No such file or directory<br>
> > #include <math.h><br>
> > ^<br>
> > compilation terminated.<br>
> ><br>
> > ----OR-----<br>
> ><br>
> > /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10:<br>
> > fatal error: features.h: No such file or directory<br>
> > 39 | #include <features.h><br>
> > | ^~~~~~~~~~~~<br>
> > compilation terminated.<br>
> ><br>
> > The cpp code seems to work fine in login node, as it gives out the value<br>
> > of pi upon execution. I am contacting the hpc admin to resolve this issue.<br>
> ><br>
> > I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh)<br>
> > and the output file (slurn-117473.out), if you would like to have a look at<br>
> > it.<br>
> ><br>
> > Please let me know if I should try something different to get this working.<br>
> ><br>
> > Regards<br>
> > Shamim Haque<br>
> > Senior Research Fellow (SRF)<br>
> > Department of Physics<br>
> > IISER Bhopal<br>
> ><br>
> > ᐧ<br>
> ><br>
> > On Mon, May 8, 2023 at 7:25 PM Shamim Haque 1910511 <<a href="mailto:shamims@iiserb.ac.in" target="_blank">shamims@iiserb.ac.in</a>><br>
> > wrote:<br>
> > <br>
> >> Thanks Steve. I'll make the changes and try again. I'll let you know the<br>
> >> outcome.<br>
> >><br>
> >> Regards<br>
> >> Shamim Haque<br>
> >> Senior Research Fellow (SRF)<br>
> >> Department of Physics<br>
> >> IISER Bhopal<br>
> >><br>
> >> ᐧ<br>
> >><br>
> >> On Mon, May 8, 2023 at 7:21 PM Steven R. Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> >> wrote:<br>
> >> <br>
> >>> That tends to make me think you aren't using the compiler you think<br>
> >>> you're using. You could put full paths in the .cfg files and recompile from<br>
> >>> scratch.<br>
> >>><br>
> >>> i.e.<br>
> >>><br>
> >>> CXX = /full/path/to/icc<br>
> >>><br>
> >>> --Steve<br>
> >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote:<br>
> >>><br>
> >>> Yes, this gives the value of Pi successfully, before starting the<br>
> >>> compilation:<br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine: paramganga3 Using<br>
> >>> configuration: sim Reconfiguring sim Writing configuration to:<br>
> >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList Cactus -<br>
> >>> version: 4.12.0 Reconfiguring sim. *<br>
> >>> *.*<br>
> >>> *.*<br>
> >>> *.*<br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>> *checking for M_PI... no configure: error: M_PI not defined. Try adding<br>
> >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config make: ***<br>
> >>> [sim-config] Error 2 *<br>
> >>><br>
> >>><br>
> >>> Shamim Haque<br>
> >>> Senior Research Fellow (SRF)<br>
> >>> Department of Physics<br>
> >>> IISER Bhopal<br>
> >>><br>
> >>> ᐧ<br>
> >>><br>
> >>> On Thu, May 4, 2023 at 12:29 AM Steven Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> >>> wrote:<br>
> >>> <br>
> >>>> So, sanity check, can you compile the following program outside of<br>
> >>>> Cactus?<br>
> >>>><br>
> >>>> #include <math.h><br>
> >>>> #include <stdio.h><br>
> >>>><br>
> >>>> int main() {<br>
> >>>> printf("%f\n", M_PI);<br>
> >>>> return 0;<br>
> >>>> }<br>
> >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote:<br>
> >>>><br>
> >>>> Dear Steve,<br>
> >>>><br>
> >>>> I tried gcc (10 and 11) as well and I am stuck with the following error:<br>
> >>>> *configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to<br>
> >>>> CPPFLAGS.*<br>
> >>>><br>
> >>>> This also happened for Intel (2020 and 2019). I have attached both the<br>
> >>>> output files here.<br>
> >>>><br>
> >>>> Please ignore the out file in the first email, I have uploaded another<br>
> >>>> out file by mistake. The rest of the files are correct in the first mail.<br>
> >>>><br>
> >>>> Regards<br>
> >>>> Shamim Haque<br>
> >>>> Senior Research Fellow (SRF)<br>
> >>>> Department of Physics<br>
> >>>> IISER Bhopal<br>
> >>>><br>
> >>>> ᐧ<br>
> >>>><br>
> >>>> On Wed, May 3, 2023 at 8:04 PM Steven Brandt <<a href="mailto:sbrandt@cct.lsu.edu" target="_blank">sbrandt@cct.lsu.edu</a>><br>
> >>>> wrote:<br>
> >>>> <br>
> >>>>> I notice from the output that your compiler claims "limits.h" is<br>
> >>>>> missing. Possibly there's something wrong with your icc setup? Maybe you<br>
> >>>>> should try using gcc / gfortran instead.<br>
> >>>>><br>
> >>>>> --Steve<br>
> >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote:<br>
> >>>>><br>
> >>>>> Dear Frank,<br>
> >>>>><br>
> >>>>> I added the alias pattern for the computing nodes and now ETK can<br>
> >>>>> detect the cluster (checked by asking "whoami") during the batch queuing.<br>
> >>>>> I'll get in touch with the admins to include 'patch'.<br>
> >>>>><br>
> >>>>> However, the problem still persists, having assured that the correct<br>
> >>>>> machine file and option list are being used during the compilation.<br>
> >>>>><br>
> >>>>> Regards<br>
> >>>>> Shamim Haque<br>
> >>>>> Senior Research Fellow (SRF)<br>
> >>>>> Department of Physics<br>
> >>>>> IISER Bhopal<br>
> >>>>><br>
> >>>>> ᐧ<br>
> >>>>><br>
> >>>>> On Wed, May 3, 2023 at 3:49 PM Frank Loeffler <<br>
> >>>>> <a href="mailto:frank.loeffler@uni-jena.de" target="_blank">frank.loeffler@uni-jena.de</a>> wrote:<br>
> >>>>> <br>
> >>>>>> 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... <br>
> >>>>>> yeschecking <br>
> >>>>>> >whether the Fortran compiler (gfortran ) is a cross-compiler... <br>
> >>>>>> nochecking <br>
> >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*) for<br>
> >>>>>> >CCTK_PointerTo... yeschecking how to run the C preprocessor... <br>
> >>>>>> cppchecking <br>
> >>>>>> >for ANSI C header files... nochecking for C99 features... <br>
> >>>>>> yeschecking for <br>
> >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding <br>
> >>>>>> -D_XOPEN_SOURCE to <br>
> >>>>>> >CPPFLAGS.*<br>
> >>>>>> ><br>
> >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. <br>
> >>>>>> This <br>
> >>>>>> >error is consistent if we set up using Intel Compiler (2020 or <br>
> >>>>>> 2019), or <br>
> >>>>>> >gcc (11 or 10). I have attached the outfile, error file, machine <br>
> >>>>>> 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 <br>
> >>>>>> directory, <br>
> >>>>>> >does "setup-silent", and then executes the build command. Is this <br>
> >>>>>> 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 <br>
> >>>>>> sbatch <br>
> >>>>>> >queue for reference. <br>
> >>>>>><br>
> >>>>>> I might be wrong, but setup-silent will not use your machine file<br>
> >>>>>> which<br>
> >>>>>> contains all the compiler flags, but will setup something "from<br>
> >>>>>> scratch"<br>
> >>>>>> instead. According to the logs, this will be, e.g., in<br>
> >>>>>><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<br>
> >>>>>> 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<br>
> >>>>>> instead<br>
> >>>>>> the correct cluster configuration is found and used automatically. In<br>
> >>>>>> order to do that, look at examples of 'aliaspattern' in the<br>
> >>>>>> mdb/machines<br>
> >>>>>> directory. An alternative would be to tell simfactory specifically<br>
> >>>>>> 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<br>
> >>>>>> 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>
> >>>>>> <br>
> >>>>> _______________________________________________<br>
> >>>>> Users mailing listUsers@einsteintoolkit.orghttp://<a href="http://lists.einsteintoolkit.org/mailman/listinfo/users" rel="noreferrer" target="_blank">lists.einsteintoolkit.org/mailman/listinfo/users</a><br>
> >>>>><br>
> >>>>> _______________________________________________<br>
> >>>>> Users mailing list<br>
> >>>>> <a href="mailto:Users@einsteintoolkit.org" target="_blank">Users@einsteintoolkit.org</a><br>
> >>>>> <a href="https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$</a> <br>
> >>>>> <br>
> >>>> <br>
<br>
<br>
Yours,<br>
Roland<br>
<br>
-- <br>
My email is as private as my paper mail. I therefore support encrypting<br>
and signing email messages. Get my PGP key from <a href="http://pgp.mit.edu" rel="noreferrer" target="_blank">http://pgp.mit.edu</a> .<br>
</blockquote></div>