Dear all,
The error which is "CalcError: sander.APBS failed with prmtop ./lig.prmtop" occurred when I used MMPBSA.py.MPI script in the condition of CHARMM force field. The input file is:
&general
startframe=1, endframe=100, interval=1,
keep_files=2,search_path=1,verbose=1,
/
&pb
istrng=0.1,sander_apbs=1,radiopt=0
/
For the complex and receptor parts, the corresponding energies are outputed in _MMPBSA_*_pb.mdout.* files, But in calculation ligand part, the error message is:
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: compute-0-5.local (PID 1210)
MPI_COMM_WORLD rank: 0
If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[compute-0-5.local:01209] 1 more process has sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[compute-0-5.local:01209] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[compute-0-5.local:01209] 6 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[compute-0-5:12630] *** Process received signal ***
[compute-0-5:12630] Signal: Segmentation fault (11)
[compute-0-5:12630] Signal code: Address not mapped (1)
[compute-0-5:12630] Failing at address: 0x12d6b818
CalcError: /home/duanbg/software/amber11/bin/sander.APBS failed with prmtop ./lig.prmtop!
Whether is this message to show that the CalcError is related with MPI program installation or something?
In addition, if I saved the temporary files in calculation binding energy using MMPBSA method, could I continue to calculate ligand part when results of complex and receptor is done well? Thanks in advance!
Best wishes
Duan Baogen
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Received on Thu Apr 04 2013 - 19:30:03 PDT
