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Problem of make: ": catastrophic error"？？？ [SOLVED]
Posted: Wed Nov 27, 2013 4:14 am
by ljludwig
There is no problem at all at the stage of configuration, and the make install is also totally OK if I do it in another cluster.
However, the problem I am facing is :
: catastrophic error: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for nmsq_pure_gkk_sumfs.F90 (code 1)
Which I don't understand at all. Any hint of this problem?
The configure I am using:
./configure --prefix=/home/XXX/abinit-7.4.3 --enable-64bit-flags=yes --enable-mpi=yes --enable-mpi-io=yes --with-mpi-prefix="/opt/intel-openmpi" cc="/opt/intel-openmpi/bin/mpicc" fc="/opt/intel-openmpi/bin/mpif90" --with-fft-flavor=fftw3 --with-fft-libs="-L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-linalg-flavor=mkl --with-linalg-libs="-L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-dft-flavor="wannier90"
Many thanks!!!
Re: Problem of make: ": catastrophic error"？？？
Posted: Fri Nov 29, 2013 9:34 am
by jbeuken
Hi,
which version of intel compile you use ? ( for 13 : >= 13.0.1 or >= 13.1.3 )
try also the compile the "nmsq_pure_gkk_sumfs.F90" without optimization ( -O0 )
jmb
Re: Problem of make: ": catastrophic error"？？？
Posted: Fri Nov 29, 2013 8:50 pm
by ljludwig
Hell! Thank you for your prompt response.
From the documentation, I can see that the version from "csupport" is :
"Package ID: l_ccompxe_2011.11.339 l_ccompxe_12.1.5.339
This package contains:
Intel(R) C++ Compiler XE 12.1 Update 5 for Linux*
Intel(R) Debugger 12.1 Update 5 for Linux*"
the version from "mkl support" is
"Package ID: l_mkl_10.3.11.339 l_ccompxe_2011.11.339 l_fcompxe_2011.11.339
This package contains:
Intel(R) Math Kernel Library 10.3 Update 11 for Linux* OS"
Are these version too low to be correctly complied? Thanks a lot.
Re: Problem of make: ": catastrophic error"？？？
Posted: Mon Dec 02, 2013 3:49 pm
by jbeuken
Hi,
I succeeded in compiling ABINIT 7.4.3 with Intel 12.1.4 or 12.1.7 , 10.3 mkl and OpenMPI 1.6 (but not tested with IMPI (non-free software))!
Then, i guess 12.1.5 has also worked …
I use your configure cmd :
Code: Select all
./configure \
--enable-64bit-flags=yes \
--enable-mpi=yes \
--enable-mpi-io=yes \
--with-mpi-prefix="/usr/local/openmpi_intel12" \
--with-fft-flavor=fftw3 \
--with-fft-libs="-L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" \
--with-linalg-flavor=mkl \
--with-linalg-libs="-L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" \
--with-dft-flavor="wannier90"
the compilation and tests seq/paral are ok ( except a problem with wannier90#11
)
can you post your config.log ?
jmb
Re: Problem of make: ": catastrophic error"？？？
Posted: Thu Dec 05, 2013 9:10 pm
by ljludwig
Thank you very much!!! I've attached the config.log here.
As to the compiler version, the cluster admin says that despite it was version 12.1, they keep it updated regularly. I'm not sure what exactly that supposes to mean, but it seems the version could be newer. (which I don't understand since the configure says it is 12.1).
Thank you in advance!
Ludwig
Re: Problem of make: ": catastrophic error"？？？
Posted: Thu Dec 05, 2013 10:15 pm
by ljludwig
This time I actually tried 7.2.2, but still have the same error:
: catastrophic error: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for nmsq_pure_gkk_sumfs.F90 (code 1)
make[4]: *** [nmsq_pure_gkk_sumfs.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/home/ludwig/softwares/abinit-7.2.2/src/77_ddb'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/ludwig/softwares/abinit-7.2.2/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ludwig/softwares/abinit-7.2.2'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/ludwig/softwares/abinit-7.2.2'
make: *** [multi] Error 2
Re: Problem of make: ": catastrophic error"？？？
Posted: Thu Dec 05, 2013 10:36 pm
by ljludwig
One more thing worthwhile mention, that even if I compile as:
./configure --prefix=/home/ludwig/abinit-7.4.3 --enable-64bit-flags=yes --enable-mpi=yes --enable-mpi-io=yes --with-mpi-prefix="/opt/intel-openmpi/" --with-dft-flavor=none
which is quite simple, the same error still exists during "make" .
: catastrophic error: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for nmsq_pure_gkk_sumfs.F90 (code 1)
make[4]: *** [nmsq_pure_gkk_sumfs.o] Error 1
I'll then try a minimal sequantial make and see how it goes...
Re: Problem of make: ": catastrophic error"？？？
Posted: Thu Dec 05, 2013 11:04 pm
by ljludwig
However, fortunately, when I do the simplest make, without 64bit flag or mpi, it works!!!
"--prefix=/home/ludwig/abinit-7.4.3 --with-dft-flavor=none"
Therefore, I think the problem comes from the mpi. I'll try another mpi and see.
Re: Problem of make: ": catastrophic error"？？？
Posted: Thu Dec 05, 2013 11:43 pm
by ljludwig
Eventually, I used MVAPICH2, instead of openmpi, and it worked to the end of make!!! (7.4.3 tested, 7.2.2 not tested)
I'm not sure what is the origin of the problem, though.
Many thanks!!!