The scheme #2 and #2a seem not working for AMBER on Stampede

[taisung]

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]

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]

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

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