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If you run into troubles, it is always a good habit to report the following information:
as well as the value of the relevant environmental variables, such OMP_NUM_THREADS, etc.
This information helps us a lot when figuring out what is going on with your compilation
- the way build.mrcc was invoked
- the output of build.mrcc
- compiler version (for example: ifort -V, gfortran -v)
- blas/lapack versions
- as well as gcc and glibc versions
as well as the value of the relevant environmental variables, such OMP_NUM_THREADS, etc.
This information helps us a lot when figuring out what is going on with your compilation
Segfault with GCC 5.4.0/MKL 2016.4.072
- jgonthier
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6 years 10 months ago #502
by jgonthier
Segfault with GCC 5.4.0/MKL 2016.4.072 was created by jgonthier
Dear MRCC community,
I am trying to install MRCC on my local cluster, with the idea of using it both as standalone and through the Psi4 interface.
I am using GCC 5.4.0 and Intel MKL 2016.4.072 that I load through the cluster's module system. I modified the option linpacklib in the build.mrcc.config script for GNU compilers as such:
linpacklib="-lmkl_blas95_ilp64 -lmkl_lapack95_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lgomp"
I then build MRCC with:
./build.mrcc GNU -pOMP -f/clusterfs/mhg/jgonthier/mrcc_inst >& buildout
MRCC build and links fine, but a number of tests are failing with SIGSEGV error message, both with OMP_NUM_THREADS=2 and OMP_NUM_THREADS=1. The first to fail is C10H22_STO-3G_LCCSD_mrcc_smallmem.
I re-built MRCC with the debug flag:
./build.mrcc GNU -pOMP -g -f/clusterfs/mhg/jgonthier/mrcc_inst >& buildout
C10H22_STO-3G_LCCSD_mrcc_smallmem still fails. The following error message is printed:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2B10D3728C57
#1 0x2B10D3727E50
#2 0x2B10D43EA26F
#3 0x482CD8 in symanal_ at mrcc.f:2452
#4 0x483642 in occgraph_ at mrcc.f:2403
#5 0x485011 in gconfig_ at mrcc.f:2222
#6 0x48D6BE in mrcc at mrcc.f:780
Does anyone have a suggestion on how to solve this issue?
I am trying to install MRCC on my local cluster, with the idea of using it both as standalone and through the Psi4 interface.
I am using GCC 5.4.0 and Intel MKL 2016.4.072 that I load through the cluster's module system. I modified the option linpacklib in the build.mrcc.config script for GNU compilers as such:
linpacklib="-lmkl_blas95_ilp64 -lmkl_lapack95_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lgomp"
I then build MRCC with:
./build.mrcc GNU -pOMP -f/clusterfs/mhg/jgonthier/mrcc_inst >& buildout
MRCC build and links fine, but a number of tests are failing with SIGSEGV error message, both with OMP_NUM_THREADS=2 and OMP_NUM_THREADS=1. The first to fail is C10H22_STO-3G_LCCSD_mrcc_smallmem.
I re-built MRCC with the debug flag:
./build.mrcc GNU -pOMP -g -f/clusterfs/mhg/jgonthier/mrcc_inst >& buildout
C10H22_STO-3G_LCCSD_mrcc_smallmem still fails. The following error message is printed:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2B10D3728C57
#1 0x2B10D3727E50
#2 0x2B10D43EA26F
#3 0x482CD8 in symanal_ at mrcc.f:2452
#4 0x483642 in occgraph_ at mrcc.f:2403
#5 0x485011 in gconfig_ at mrcc.f:2222
#6 0x48D6BE in mrcc at mrcc.f:780
Does anyone have a suggestion on how to solve this issue?
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- kallay
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- Mihaly Kallay
6 years 10 months ago #503
by kallay
Best regards,
Mihaly Kallay
Replied by kallay on topic Segfault with GCC 5.4.0/MKL 2016.4.072
We have reproduced the error and we will look at it.
You should use the Intel compiler or the precompiled binaries.
You should use the Intel compiler or the precompiled binaries.
Best regards,
Mihaly Kallay
The following user(s) said Thank You: jgonthier
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- jgonthier
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6 years 10 months ago #504
by jgonthier
Replied by jgonthier on topic Segfault with GCC 5.4.0/MKL 2016.4.072
I was only today able to compile and test with Intel compilers: everything seems to be fine now. Only the Libxc tests failed, as expected since I do not have it installed.
Thank you very much for your help.
Thank you very much for your help.
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