On Wed, Jul 03, 2019, Francesca Lønstad 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 - 05:30:03 PDT
