[Users] Compilation Error in cluster ParamGanga
Shamim Haque 1910511
shamims at iiserb.ac.in
Thu May 11 15:28:33 CDT 2023
Hello Roland,
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:
*#include <math.h>#include <stdio.h>int main() { printf("%f\n",
M_PI); return 0;}*
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:
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.
I have reported this problem to the HPC admin and await their response.
Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal
ᐧ
On Fri, May 12, 2023 at 12:20 AM Roland Haas <rhaas at illinois.edu> wrote:
> Hello all,
>
> Since the error is a missing M_PI and the configure script already
> gives a suggested fix:
>
> Try adding -D_XOPEN_SOURCE to CPPFLAGS.
>
> have you tried adding:
>
> CPPFLAGS=-D_XOPEN_SOURCE
>
> to your option list file before compiling?
>
> Yours,
> Roland
>
> > Thanks Steve. I have raised complaint to the admin about this issue.
> >
> > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt <sbrandt at cct.lsu.edu>
> wrote:
> >
> > > 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 <
> shamims at iiserb.ac.in>
> > > 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 <sbrandt at cct.lsu.edu>
> > >> 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 <sbrandt at cct.lsu.edu>
> > >>> 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 <sbrandt at cct.lsu.edu>
> > >>>> 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 <
> > >>>>> frank.loeffler at 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
> > >>>>>>
> > >>>>>>
> > >>>>> _______________________________________________
> > >>>>> Users mailing listUsers at einsteintoolkit.orghttp://
> lists.einsteintoolkit.org/mailman/listinfo/users
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> Users mailing list
> > >>>>> Users at einsteintoolkit.org
> > >>>>>
> https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$
> > >>>>>
> > >>>>
>
>
> Yours,
> Roland
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://pgp.mit.edu .
>
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