New subject: Compilation Error in cluster ParamGanga

11 May 2023


      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@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@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@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@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@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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Re: [Users] Compilation Error in cluster ParamGanga