Re: [AMBER] SIGSEVV error on test_at_serial for QMMM

From: Francesca Lønstad Bleken <>
Date: Thu, 4 Jul 2019 05:42:38 +0000


It is CENTOS7 and the following modules loaded

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
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,

Date: Wed, 3 Jul 2019 08:04:36 -0400
From: David A Case <>
Subject: Re: [AMBER] SIGSEVV error on test_at_serial for QMMM
        interface and miniconda installation problem thrugh amberTools
To: AMBER Mailing List <>
Message-ID: <>
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
>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
> 00002BA42474B522 for__signal_handl Unknown Unknown
>libpthread-2.17.s 00002BA426F4D5D0 Unknown Unknown Unknown
> 00002BA40CB4F264 get_qm2_forces_re Unknown Unknown
> 00002BA40CB3D1EA sander_api_mp_san Unknown Unknown
>testf 0000000000403AEC Unknown Unknown Unknown
>testf 0000000000402322 Unknown Unknown Unknown
> 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
> 00002ADC53FE2522 for__signal_handl Unknown Unknown
>libpthread-2.17.s 00002ADC567E45D0 Unknown Unknown Unknown
> 00002ADC3C3E6264 get_qm2_forces_re Unknown Unknown
> 00002ADC3C3D41EA sander_api_mp_san Unknown Unknown
>testf2 0000000000403CE7 Unknown Unknown Unknown
>testf2 00000000004022A2 Unknown Unknown Unknown
> 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
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