From a6a51d81abae2685e8438c4a0f500dfe8111c8c6 Mon Sep 17 00:00:00 2001
From: "Mads M. Pedersen" <mmpe@dtu.dk>
Date: Tue, 11 Dec 2018 08:20:49 +0100
Subject: [PATCH] Removed pathlib dependency from PBSMultiRunner
---
wetb/utils/cluster_tools/pbsfile.py | 9 ++++-----
wetb/utils/tests/test_pbs_file.py | 9 ++++-----
2 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/wetb/utils/cluster_tools/pbsfile.py b/wetb/utils/cluster_tools/pbsfile.py
index 8a28d1c3..16217c57 100644
--- a/wetb/utils/cluster_tools/pbsfile.py
+++ b/wetb/utils/cluster_tools/pbsfile.py
@@ -137,7 +137,6 @@ class PBSMultiRunner(PBSFile):
import os
import glob
import numpy as np
- from pathlib import Path
import re
# find available nodes
@@ -150,7 +149,8 @@ class PBSMultiRunner(PBSFile):
def get_info(f):
try:
- return (f,) + pat.match(Path(f).read_text()).groups()
+ with open(f) as fid:
+ return (f,) + pat.match(fid.read()).groups()
except Exception:
return (f, f.replace('.in', '.out'), '00:30:00')
pbs_info_lst = map(get_info, pbs_files)
@@ -164,12 +164,11 @@ class PBSMultiRunner(PBSFile):
def start_jobs(self):
import os
- from pathlib import Path
import multiprocessing
import platform
import time
-
- pbs_info_lst = eval(Path('pbs.dict').read_text())[platform.node()]
+ with open('pbs.dict') as fid:
+ pbs_info_lst = eval(fid.read())[platform.node()]
arg_lst = ['echo starting %s && mkdir -p %s && env PBS_JOBID=$PBS_JOBID %s &> %s && echo finished %s' %
(f, os.path.dirname(o), f, o, f) for f, o, _ in pbs_info_lst]
print(arg_lst[0])
diff --git a/wetb/utils/tests/test_pbs_file.py b/wetb/utils/tests/test_pbs_file.py
index 3f8e4fa1..117a631b 100644
--- a/wetb/utils/tests/test_pbs_file.py
+++ b/wetb/utils/tests/test_pbs_file.py
@@ -89,7 +89,6 @@ pwd
echo "import os
import glob
import numpy as np
-from pathlib import Path
import re
# find available nodes
@@ -102,7 +101,8 @@ pat = re.compile(r'[\s\S]*#\s*PBS\s+-o\s+(.*)[\s\S]*(\d\d:\d\d:\d\d)[\s\S]*')
def get_info(f):
try:
- return (f,) + pat.match(Path(f).read_text()).groups()
+ with open(f) as fid:
+ return (f,) + pat.match(fid.read()).groups()
except Exception:
return (f, f.replace('.in', '.out'), '00:30:00')
pbs_info_lst = map(get_info, pbs_files)
@@ -122,12 +122,11 @@ do
ssh -T $node << EOF &
cd /home/user/tmp
python -c "import os
-from pathlib import Path
import multiprocessing
import platform
import time
-
-pbs_info_lst = eval(Path('pbs.dict').read_text())[platform.node()]
+with open('pbs.dict') as fid:
+ pbs_info_lst = eval(fid.read())[platform.node()]
arg_lst = ['echo starting %s && mkdir -p %s && env PBS_JOBID=$PBS_JOBID %s &> %s && echo finished %s' %
(f, os.path.dirname(o), f, o, f) for f, o, _ in pbs_info_lst]
print(arg_lst[0])
--
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