[Users] Compilation Error in cluster ParamGanga

Shamim Haque 1910511 shamims at iiserb.ac.in
Thu May 11 12:54:33 CDT 2023 

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
>>>>>>
>>>>>>
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>>>>
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