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radical-cybertools / radical.repex.at

This is the github location for RepEx developed by the RADICAL team in conjunction with the York Lab.
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The scheme #2 and #2a seem not working for AMBER on Stampede #8

Closed taisung closed 10 years ago

taisung commented 10 years ago

I tried the amber example with Scheme #2 and #2a on Stampede and the exchange part was not executed with the following error:

File "launch_simulation_scheme_2_amber.py", line 55, in pilot_kernel.run_simulation( replicas, pilot_object, session, md_kernel ) File "/usr/people/taisung/Data/CDI-SAGA/RepEx/src/radical/repex/pilot_kernels/pilot_kernel_scheme_2.py", line 119, in run_simulation swap_matrix = self.compose_swap_matrix(replicas) File "/usr/people/taisung/Data/CDI-SAGA/RepEx/src/radical/repex/pilot_kernels/pilot_kernel_scheme_2.py", line 67, in compose_swap_matrix f = open(column_file) IOError: [Errno 2] No such file or directory: 'matrix_column_0_0.dat'

antonst commented 10 years ago

Hi Taisung, to me this appears as first simulation cycle never being finished and in the result of that no data has been transferred back. Is this correct? Do you see Amber output files in your working directory? Can you please post your input file here as well?

Thanks, Antons

taisung commented 10 years ago

Hi Antons,

           In fact, I just used your examples.  Both amber and namd finished the first simulation but no exchange happened.

Taisung

From: Antons [mailto:notifications@github.com] Sent: Friday, July 18, 2014 11:39 AM To: radical-cybertools/RepEx Cc: taisung Subject: Re: [RepEx] The scheme #2 and #2a seem not working for AMBER on Stampede (#8)

Hi Taisung, to me this appears as first simulation cycle never being finished and in the result of that no data has been transferred back. Is this correct? Do you see Amber output files in your working directory? Can you please post your input file here as well?

Thanks, Antons

— Reply to this email directly or view it on GitHub https://github.com/radical-cybertools/RepEx/issues/8#issuecomment-49445354 . https://github.com/notifications/beacon/2932347__eyJzY29wZSI6Ik5ld3NpZXM6QmVhY29uIiwiZXhwaXJlcyI6MTcyMTMxNzE1MiwiZGF0YSI6eyJpZCI6MzczNzg5NTV9fQ==--29d5145ce09adc990f622b54a24f019ac4ef18e7.gif