Re: [SIESTA-L] problem with compile siesta-4.0

Tue, 31 May 2016 01:58:15 -0700

Dear Nick,

I finally solved the problem but switched back to ifort15.

The compilation works fine but when running the si001 test, I got the following error:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
.                  0000000000BC53F1  Unknown               Unknown  Unknown
.                  0000000000BC38A7  Unknown               Unknown  Unknown
.                  0000000000B6C3A4  Unknown               Unknown  Unknown
.                  0000000000B6C1B6  Unknown               Unknown  Unknown
.                  0000000000B1A616  Unknown               Unknown  Unknown
.                  0000000000B20E1D  Unknown               Unknown  Unknown
libpthread.so.0    00007F0DD09E68D0  Unknown               Unknown  Unknown
.                  00000000006D8BAF  Unknown               Unknown  Unknown

Stack trace terminated abnormally.

The output is attached, such as the arch.make file.

Any Idea?

Thanks,

Rémi

Attachment: arch.make
Description: Binary data

Attachment: si001.log
Description: Binary data




Le 30 mai 2016 à 20:38, Nick Papior <[email protected]> a écrit :



2016-05-30 20:29 GMT+02:00 remi marchal <[email protected]>:
Dear Nick,

Using the ifort16, I have the following error in the config.log of Fox.

ifort: error #10236: File not found:  '/exe:conftest’

I never had such kind of problem.

Do you have any hint concerning this problem.
You can't use openmpi compiled with intel 15 and then use intel 16. You need to recompile openmpi with intel 16... 

Do NOT mix intel compiler suites:
PATH: /opt/intel/composer_xe_2015.6.233/bin/intel64
PATH: /opt/intel/composer_xe_2015.6.233/debugger/gdb/intel64_mic/bin
PATH: /opt/intel/compilers_and_libraries_2016.3.210/linux/bin/intel64
PATH: /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/bin

It seems like you have two versions added (and in the 2016 version also mpi is sourced, which you do not want...
 

You will find the config.log of Fox attached.
See this line:
 configure:1955: /cluster_cti/utils/openmpi/openmpi-1.10.2/bin/mpif90 -V </dev/null >&5
Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.6.233 Build 20151119
Copyright (C) 1985-2015 Intel Corporation.  All rights reserved.


Regards,

Rémi




Le 30 mai 2016 à 08:58, Nick Papior <[email protected]> a écrit :

FYI, ifort16 is supported (I can compile using it just fine...)

But if you can easier compile using ifort15, then proceed with that.

If you want help regarding ifort16, please:
1. Ensure that your OpenMPI installation has been compiled with ifort16 as well
2. Try without static linking, 
3. Use intel blas (-lmkl_blas95_lp64)
4. Use intel lapack  (-lmkl_lapack95_lp64)
5. Use intel scalapack (-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64)
6. Add dependency intel libraries (-lmkl_intel_lp64 -lmkl_core -lmkl_sequential)


2016-05-30 8:41 GMT+02:00 remi marchal <[email protected]>:
Dear Nick,

Indeed, after checking the config.log, I seen the problem.

The problem seems to be related to the version of the intel compiler. Indeed, the latest ifort16 version seems to be unsupported.

Switching to ifort15 solve the problem.

Thanks a lot,

Rémi





Le 28 mai 2016 à 08:01, Nick Papior <[email protected]> a écrit :

See further down... 

--

Kind regards Nick Papior
On 27 May 2016 19:59, "remi marchal" <[email protected]> wrote:
>
> Dear siesta users,
>
> I have some troubles to compile siesta-4 on our debian cluster.
>
> I try to compile it with openmpi and ifort and here is the message I get:
>
> the following error:
>
> Compilation architecture to be used: 
> If this is not what you want, create the right
> arch.make file using the models in Src/Sys
>
> Hit ^C to abort...
> (cd FoX; touch arch.make ; \
>          CONFIGURE="/home/admincluster/compile-siesta/siesta-4.0-b1/Src/FoX/configure"; \
>          $CONFIGURE VPATH="/home/admincluster/compile-siesta/siesta-4.0-b1/Src/FoX" \
>          FC="/cluster_cti/utils/openmpi/openmpi-1.10.2/bin/mpif90" FCFLAGS="-g" \
>          --enable-wcml  || false )
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for linker flag to name executables... -o 
> checking for Fortran compiler default output file name... conftest
> checking whether the Fortran compiler works... configure: error: cannot run Fortran compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details.
Do this to get information about the problem. Check for any errors in that file. 
Note the file is in the FoX directory. 
> Makefile:184: recipe for target 'FoX/.config' failed
> make: *** [FoX/.config] Error 1
>
> my arch.make is attached.
>
> Does anyone already seen such kind of problems
>
> Regards
>
> Rémi
>
>
>
>





-- 
Kind regards Nick





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Kind regards Nick

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