[Users] Compilation Error in cluster ParamGanga
Steven R. Brandt
sbrandt at cct.lsu.edu
Thu May 11 12:48:53 CDT 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 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
>>>>
>>>>
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