Hi AMBER Developers,
I'm new to the MD simulations. I'm trying to perform tutorials of Amber.
During the tutorial Replica Exchange, I have encountered few errors.
Please help me to understand.
I gave the following command to run the Replica Exchange simulation (as
mentioned in the tutorial)
mpirun -np 8 $AMBERHOME/bin/sander.MPI -ng 8 -groupfile
equilibrate.groupfile
It shows me the following error.
Error: specified more groups ( 8 ) than the number of
processors ( 1 ) !
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
Here are the details of my workstation:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 32
On-line CPU(s) list: 0-31
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 63
Model name: Intel(R) Xeon(R) CPU E5-2640 v3 . 2.60GHz
Stepping: 2
CPU MHz: 1229.223
CPU max MHz: 3400.0000
CPU min MHz: 1200.0000
BogoMIPS: 5199.62
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 20480K
NUMA node0 CPU(s): 0-7,16-23
NUMA node1 CPU(s): 8-15,24-31
I have further tried few other combinations by increasing the number of
processor from 8 to 24 in multiples of 8. However, the job runs only
when we use "-ng 1" for groupfile.
Regards,
Munazzah Fatima Ansari
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Received on Tue Nov 01 2022 - 23:00:02 PDT
