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bis-aria
ariaec
Commits
095d8e90
Commit
095d8e90
authored
Mar 21, 2019
by
Fabrice Allain
Browse files
refactor: use vformat function to generate csh scripts
parent
a036e7f5
Changes
1
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Inline
Side-by-side
aria/core/cns.py
View file @
095d8e90
...
@@ -82,42 +82,42 @@ PLAN = 'plan.tbl'
...
@@ -82,42 +82,42 @@ PLAN = 'plan.tbl'
CNS_OUTPUT_PATH_NAME
=
'cns'
CNS_OUTPUT_PATH_NAME
=
'cns'
CSH_SCRIPT_REFINE
=
'''
\
CSH_SCRIPT_REFINE
=
'''
\
#!
%(
sge_job_shell
)s
#!
{
sge_job_shell
}
# SGE/PBS/SLURM/LFS facility
# SGE/PBS/SLURM/LFS facility
#$ -N
%(
sge_job_name
)s
#$ -N
{
sge_job_name
}
#$ -S
%(
sge_job_shell
)s
#$ -S
{
sge_job_shell
}
#PBS -N
%(
sge_job_name
)s
#PBS -N
{
sge_job_name
}
#PBS -S
%(
sge_job_shell
)s
#PBS -S
{
sge_job_shell
}
#BSUB -J
%(
sge_job_name
)s
#BSUB -J
{
sge_job_name
}
#BSUB -L
%(
sge_job_shell
)s
#BSUB -L
{
sge_job_shell
}
#BSUB -oo refine.lsf.out
#BSUB -oo refine.lsf.out
#BSUB -eo refine.lsf.err
#BSUB -eo refine.lsf.err
#SBATCH -o refine.%j.slurm.out
#SBATCH -o refine.%j.slurm.out
#SBATCH -e refine.%j.slurm.err
#SBATCH -e refine.%j.slurm.err
#SBATCH -J
%(
sge_job_name
)s
#SBATCH -J
{
sge_job_name
}
#SBATCH --ignore-pbs
#SBATCH --ignore-pbs
# results will be stored here
# results will be stored here
setenv NEWIT
%(
iteration_path
)s
setenv NEWIT
{
iteration_path
}
# project path
# project path
setenv RUN
%(
cns_resource_path
)s
setenv RUN
{
cns_resource_path
}
# individual run.cns is stored here
# individual run.cns is stored here
setenv RUN_CNS
%(
cns_working_dir
)s
setenv RUN_CNS
{
cns_working_dir
}
# path of ARIA2 cns protocos (for RAMA)
# path of ARIA2 cns protocos (for RAMA)
setenv RAMA_DATA
%(
rama_data_dir
)s
setenv RAMA_DATA
{
rama_data_dir
}
# CNS working directory
# CNS working directory
cd
%(
cns_working_dir
)s
cd
{
cns_working_dir
}
# solves some NFS sync problems
# solves some NFS sync problems
cat
%(
cns_input_file
)s
> /dev/null
cat
{
cns_input_file
}
> /dev/null
# command line
# command line
%(
cns_executable
)s
<
%(
cns_input_file
)s
>!
%(
cns_output_file
)s
{
cns_executable
}
<
{
cns_input_file
}
>!
{
cns_output_file
}
touch done
touch done
'''
'''
...
@@ -167,20 +167,20 @@ Requirements = Arch == "X86_64" && OpSys == "LINUX" && Memory > 200
...
@@ -167,20 +167,20 @@ Requirements = Arch == "X86_64" && OpSys == "LINUX" && Memory > 200
CSH_SCRIPT_REFINE_CONDOR
=
'''
\
CSH_SCRIPT_REFINE_CONDOR
=
'''
\
# results will be stored here
# results will be stored here
setenv NEWIT
%(
iteration_path
)s
setenv NEWIT
{
iteration_path
}
# project path
# project path
setenv RUN
%(
cns_resource_path
)s
setenv RUN
{
cns_resource_path
}
# individual run.cns is stored here
# individual run.cns is stored here
setenv RUN_CNS
%(
cns_working_dir
)s
setenv RUN_CNS
{
cns_working_dir
}
# CNS working directory
# CNS working directory
cd
%(
cns_working_dir
)s
cd
{
cns_working_dir
}
# solves some NFS sync problems
# solves some NFS sync problems
cat
%(
cns_input_file
)s
> /dev/null
cat
{
cns_input_file
}
> /dev/null
# command line
# command line
condor_submit condor.job
condor_submit condor.job
...
@@ -194,19 +194,19 @@ cp /dev/null done
...
@@ -194,19 +194,19 @@ cp /dev/null done
CSH_SCRIPT_ANALYSIS
=
"""
\
CSH_SCRIPT_ANALYSIS
=
"""
\
# results will be stored here
# results will be stored here
setenv ANALYSIS
%(
analysis_output_path
)s
setenv ANALYSIS
{
analysis_output_path
}
# results from last iteration
# results from last iteration
setenv NEWIT
%(
iteration_path
)s
setenv NEWIT
{
iteration_path
}
# project path
# project path
setenv RUN
%(
cns_resource_path
)s
setenv RUN
{
cns_resource_path
}
# individual run.cns and output-files are stored here
# individual run.cns and output-files are stored here
setenv RUN_CNS
%(
cns_working_dir
)s
setenv RUN_CNS
{
cns_working_dir
}
# working directory
# working directory
cd
%(
cns_working_dir
)s
cd
{
cns_working_dir
}
# command line
# command line
"""
"""
...
@@ -2017,7 +2017,8 @@ class CNS(StructureEngine):
...
@@ -2017,7 +2017,8 @@ class CNS(StructureEngine):
condor_queue
=
"input = %(cns_input_file)s
\n
"
\
condor_queue
=
"input = %(cns_input_file)s
\n
"
\
"output = %(cns_output_file)s
\n
queue
\n
"
"output = %(cns_output_file)s
\n
queue
\n
"
self
.
_write_condor_script
(
d
,
condor_append
=
condor_queue
)
self
.
_write_condor_script
(
d
,
condor_append
=
condor_queue
)
script
=
CSH_SCRIPT_REFINE_CONDOR
%
d
script
=
string
.
Formatter
().
vformat
(
CSH_SCRIPT_REFINE_CONDOR
,
(),
SafeFormatDict
(
d
))
checkscript
=
string
.
Formatter
().
vformat
(
checkscript
=
string
.
Formatter
().
vformat
(
CSH_SCRIPT_CHECKPOINT
,
(),
SafeFormatDict
(
d
))
CSH_SCRIPT_CHECKPOINT
,
(),
SafeFormatDict
(
d
))
...
@@ -2030,7 +2031,8 @@ class CNS(StructureEngine):
...
@@ -2030,7 +2031,8 @@ class CNS(StructureEngine):
d
[
'sge_job_shell'
]
=
'/bin/csh -f'
d
[
'sge_job_shell'
]
=
'/bin/csh -f'
# d['sge_job_hostname'] = '%(sge_job_hostname)s'
# d['sge_job_hostname'] = '%(sge_job_hostname)s'
script
=
CSH_SCRIPT_REFINE
%
d
script
=
string
.
Formatter
().
vformat
(
CSH_SCRIPT_REFINE
,
(),
SafeFormatDict
(
d
))
d
[
'sge_checkjob_name'
]
=
sge_job_name
+
"_checkpoint"
d
[
'sge_checkjob_name'
]
=
sge_job_name
+
"_checkpoint"
checkscript
=
string
.
Formatter
().
vformat
(
checkscript
=
string
.
Formatter
().
vformat
(
CSH_SCRIPT_CHECKPOINT
,
(),
SafeFormatDict
(
d
))
CSH_SCRIPT_CHECKPOINT
,
(),
SafeFormatDict
(
d
))
...
@@ -2466,7 +2468,8 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
...
@@ -2466,7 +2468,8 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
'cns_working_dir'
:
working_dir
,
'cns_working_dir'
:
working_dir
,
'cns_executable'
:
cns_executable
}
'cns_executable'
:
cns_executable
}
csh_script
=
CSH_SCRIPT_ANALYSIS
%
csh_dict
csh_script
=
string
.
Formatter
().
vformat
(
CSH_SCRIPT_ANALYSIS
,
(),
SafeFormatDict
(
csh_dict
))
condor_append
=
'
\n
'
condor_append
=
'
\n
'
...
...
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