Hi,
It is CENTOS7 and the following modules loaded
GCCcore/8.2.0
icc/2019.1.144-GCC-8.2.0-2.31.1
iccifort/2019.1.144-GCC-8.2.0-2.31.1
impi/2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1
intel/2019a
imkl/2019.1.144-iimpi-2019a
iimpi/2019a
Python/3.7.2-GCCcore-8.2.0
OpenMPI/3.1.3-GCC-8.2.0-2.31.1
netCDF/4.6.2-iimpi-2019a
netCDF-Fortran/4.4.5-iimpi-2019a
Perl/5.28.1-GCCcore-8.2.0
FFTW/3.3.8-intel-2019a
Boost/1.70.0-iimpi-2019a
CUDA/10.1.105-GCC-8.2.0-2.31.1
And this is the configure for the serial version. (for mpi I then use -intelmpi, but these errors is before that)
yes | ./configure -noX11 intel > 01a-config_intel.log
source amber.sh
make -j 16 > 01b-make_intel.log
make install > 01c-makeinstall_intel.log
make test > 01d-maketest_intel.log
But this is the installation with the fewest errors in the make test I have seen...
Best regards,
Francesca
----------------------------------------
Date: Wed, 3 Jul 2019 08:04:36 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] SIGSEVV error on test_at_serial for QMMM
interface and miniconda installation problem thrugh amberTools
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20190703120436.zt32pta3yg6wn6er.godel.rutgers.edu>
Content-Type: text/plain; charset=iso-8859-1; format=flowed
On Wed, Jul 03, 2019, Francesca L?nstad Bleken wrote:
>
>Also for the last error I am wondering if it has to do with he python
>miniconda installed through amber.
>I have now tried on several machines and I consistently get this error
>when running ./configure the first time and installing miniconda;
>============ Error from ./configure when installing miniconda
>Done. Miniconda installed in
>/home/francesb/60-programs/amber18_mpi/amber18/miniconda
>Traceback (most recent call last):
> File "/home/francesb/60-programs/amber18_mpi/amber18/miniconda/bin/conda", line 7, in <module>
> from conda.cli import main
>ModuleNotFoundError: No module named 'conda'
>Problem installing Miniconda... see error above.
>Configure failed due to the errors above!
>==
Aargh... we have just identified this error ourselves. FWIW, it happens
on Linux but not OSX. The "configure_python" script that triggers this
has been unchanged for a long time, but what gets downloaded from
Anaconda has changed, seemingly just in the past day or so.
We will post a fix as soon as we figure out what is going wrong.
>Below are the Errors from the logfile (test_at_serial)
These errors look rather troublesome. What options did you give you the
configure script? What OS and compiler version are you using?
I don't recall having seen any report like this one before.
Thanks for your feedback....dac
>
>==========ERROR 1========
>Testing the QM/MM non-periodic interface
>forrtl: severe (174): SIGSEGV, segmentation fault occurred
>Image PC Routine Line Source
>
>libifcoremt.so.5 00002BA42474B522 for__signal_handl Unknown Unknown
>libpthread-2.17.s 00002BA426F4D5D0 Unknown Unknown Unknown
>libsander.so 00002BA40CB4F264 get_qm2_forces_re Unknown Unknown
>libsander.so 00002BA40CB3D1EA sander_api_mp_san Unknown Unknown
>testf 0000000000403AEC Unknown Unknown Unknown
>testf 0000000000402322 Unknown Unknown Unknown
>libc-2.17.so 00002BA42717C3D5 __libc_start_main Unknown Unknown
>testf 0000000000402239 Unknown Unknown Unknown
>Program error
>============ERRORs 2 and 3========
>Testing the QM/MM periodic interface (PM3-PDDG)
>| QMMM: ERROR dspevd failed to converge and returned 55
>| QMMM: Falling back on internal diagonalizer for the remainder of this run.
>| QMMM: ERROR dsyevd failed to converge and returned 55
>| QMMM: Falling back on internal diagonalizer for the remainder of this run.
>forrtl: severe (174): SIGSEGV, segmentation fault occurred
>Image PC Routine Line Source
>libifcoremt.so.5 00002ADC53FE2522 for__signal_handl Unknown Unknown
>libpthread-2.17.s 00002ADC567E45D0 Unknown Unknown Unknown
>libsander.so 00002ADC3C3E6264 get_qm2_forces_re Unknown Unknown
>libsander.so 00002ADC3C3D41EA sander_api_mp_san Unknown Unknown
>testf2 0000000000403CE7 Unknown Unknown Unknown
>testf2 00000000004022A2 Unknown Unknown Unknown
>libc-2.17.so 00002ADC56A133D5 __libc_start_main Unknown Unknown
>testf2 00000000004021B9 Unknown Unknown Unknown
>Program error
>===========ERROR 4 ========
>/bin/sh: line 1: 3447 Segmentation fault (core dumped) ./testcpp
>Program error
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Received on Wed Jul 03 2019 - 23:00:02 PDT
