Closed iparask closed 8 years ago
Can you please re-run this example? Also are you using input file from repex.examples repo?
Re-install and rerun??
I am using the command you provided in the testing protocol
Which repex version this reports?
and this is with exchange_mpi = False ?
Sorry I do not remember. What ever it was on Sunday. Now I updated it so it is 0.2.6.
This is my configuration:
{
"remd.input": {
"re_pattern": "S",
"exchange": "T-REMD",
"number_of_cycles": "3",
"number_of_replicas": "12",
"input_folder": "t_remd_inputs",
"input_file_basename": "ala10_remd",
"amber_input": "ala10.mdin",
"amber_parameters": "ala10.prmtop",
"amber_coordinates": "ala10_minimized.inpcrd",
"replica_mpi": "False",
"replica_cores": "1",
"exchange_mpi": "False",
"min_temperature": "300",
"max_temperature": "600",
"steps_per_cycle": "4000",
"download_mdinfo": "True",
"download_mdout" : "True"
}
}
and
{
"target": {
"resource": "xsede.comet",
"username" : "iparask",
"project" : "<correct_number",
"runtime" : "60",
"cleanup" : "False",
"cores" : "12"
}
}
If you specify project should be good
The project is specified. I will not put the project number on github
And it failed again. With the new run. Here is the debug file: https://gist.github.com/iparask/19ab5ed60cc5233472af
And just in case: https://gist.github.com/iparask/ceea47e4e2daac7c4806
The debug messages from the first run
Can you please try to re-run using devel and resource input file:
{
"target": {
"resource": "xsede.comet",
"username" : "octocat",
"project" : "toxic-crusaders",
"queue" : "compute",
"runtime" : "60",
"cleanup" : "False",
"cores" : "48"
}
}
and simulation input file:
{
"remd.input": {
"re_pattern": "S",
"exchange": "T-REMD",
"number_of_cycles": "3",
"input_folder": "t_remd_inputs",
"input_file_basename": "ala10_remd",
"amber_input": "ala10.mdin",
"amber_parameters": "ala10.prmtop",
"amber_coordinates_folder": "ala10_coors",
"same_coordinates": "True",
"replica_mpi": "False",
"replica_cores": "1",
"min_temperature": "300",
"max_temperature": "600",
"steps_per_cycle": "4000",
"download_mdinfo": "True",
"download_mdout" : "True"
},
"dim.input": {
"d1": {
"type" : "temperature",
"number_of_replicas": "8",
"min_temperature": "300.0",
"max_temperature": "302.0"
}
}
}
p.s. it worked for me
closed due to lack of response
I do not even remember what to run.... Specify the test or give me a link to the testing protocol
export RADICAL_REPEX_VERBOSE=info
export RADICAL_PILOT_VERBOSE=info
git clone https://github.com/radical-cybertools/radical.repex.git
cd radical.repex
git checkout devel
python setup.py install
cd examples/amber
repex-amber --input='tuu_remd_ace_ala_nme.json' --rconfig='comet.json'
you only need to modify comet.json
I get this error in the debug file:
What else do you need?