Hi,
Have all updates been applied? How was Amber configured (what flags
were used), what compilers and version, and what MPI and version are
in use?
-Dan
On Wed, Mar 16, 2016 at 10:28 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> While doing make test.parallel after installing AmberTools 15, I
> experienced the following error. I have set export DO_PARALLEL='mpirun -np
> 2' , before doing the test. Any help would be highly appreciated
>
>
> *****************************************************************************************************************************************
> make[2]: Target `test.parallel.at' not remade because of errors.
> make[2]: Leaving directory `/usr/local/amber14/test'
> make[2]: Entering directory `/usr/local/amber14/AmberTools/test'
>
> Finished test suite for AmberTools at Wed Mar 16 16:15:19 GMT 2016.
>
> make[2]: Leaving directory `/usr/local/amber14/AmberTools/test'
> 370 file comparisons passed
> 2 file comparisons failed
> 60 tests experienced errors
> Test log file saved as
> /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log
> Test diffs file saved as
> /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.diff
> make[1]: Leaving directory `/usr/local/amber14/AmberTools/test'
> ==============================================================
> /usr/local/amber14/src/Makefile not found.
> This is expected if you have not installed Amber14.
> ==============================================================
>
> ***************************************************************************************************************************************
>
>
> Part of the
> /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log is shown
> below,
>
>
>
> **************************************************************************************************************************************
> export TESTsander=/usr/local/amber14/bin/sander.MPI; cd jar_multi &&
> ./Run.jarz
>
> Running multisander version of sander Amber14
> Total processors = 2
> Number of groups = 2
>
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0 0x7F482577D467
> #1 0x7F482577DAAE
> #2 0x7F4824C8466F
> #3 0x7F482583ABE8
> #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
> #5 0x508FD7 in mdread1_ at mdread1.F90:182
> #6 0x4D6159 in sander_ at sander.F90:326
> #7 0x4D4E12 in multisander at multisander.F90:436
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = EXIT CODE: 139
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
> (signal 11)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
> ./Run.jarz: Program error
> make[2]: [test.sander.BASIC.MPI] Error 1 (ignored)
> export TESTsander=/usr/local/amber14/bin/sander.MPI; cd ti_eth2meth_gas &&
> ./Run.test1
>
> Running multisander version of sander Amber14
> Total processors = 2
> Number of groups = 2
>
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0 0x7FBD4B1CB467
> #1 0x7FBD4B1CBAAE
> #2 0x7FBD4A6D266F
> #3 0x7FBD4B288BE8
> #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
> #5 0x508FD7 in mdread1_ at mdread1.F90:182
> #6 0x4D6159 in sander_ at sander.F90:326
> #7 0x4D4E12 in multisander at multisander.F90:436
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
>
> **************************************************************************************************************************************************
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 16 2016 - 10:00:03 PDT
