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Commit
0a2dc08b
authored
May 24, 2021
by
Szeberényi Imre
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Update slurm-jupyter.patch
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19f017f9
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slurm-jupyter.patch
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0a2dc08b
diff -Naur '--exclude=*cache*' anaconda3/lib/python3.8/site-packages/slurm_jupyter/__init__.py anaconda3.new/lib/python3.8/site-packages/slurm_jupyter/__init__.py
--- anaconda3/lib/python3.8/site-packages/slurm_jupyter/__init__.py 2021-02-15 08:37:38.000000000 +0100
+++ anaconda3.new/lib/python3.8/site-packages/slurm_jupyter/__init__.py 2021-05-24 19:30:43.382213781 +0200
@@ -131,7 +131,7 @@
str: Slurm job id.
"""
- cmd = 'ssh {user}@{frontend} cat - > {tmp_dir}/{tmp_script} ; mkdir -p {tmp_dir} ; sbatch {tmp_dir}/{tmp_script} '.format(**spec)
+ cmd = 'ssh {user}@{frontend} mkdir -p {tmp_dir} ; cat - > {tmp_dir}/{tmp_script} ; sbatch {tmp_dir}/{tmp_script} '.format(**spec)
if verbose: print("script ssh transfer:", cmd, sep='\n')
@@ -336,7 +336,7 @@
Returns:
(subprocess.Popen, threading.Thread, Queue.Queue): Process, Thread and Queue.
"""
- cmd = 'ssh -L{port}:{node}.genomedk.net:{hostport} {user}@{frontend}'.format(**spec)
+ cmd = 'ssh -L{port}:{node}:{hostport} {user}@{frontend}'.format(**spec)
if verbose: print("forwarding port:", cmd)
port_p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
# we have to set stdin=PIPE even though we eodn't use it because this
@@ -385,8 +385,7 @@
"""
script = mem_script.format(**spec)
- # cmd = 'ssh {user}@{frontend} cat - > {tmp_dir}/{mem_script} ; mkdir -p {tmp_dir}'.format(**spec)
- cmd = 'ssh {user}@{frontend} cat - > {tmp_dir}/{mem_script} ; mkdir -p {tmp_dir}'.format(**spec)
+ cmd = 'ssh {user}@{frontend} mkdir -p {tmp_dir} ; cat - > {tmp_dir}/{mem_script}'.format(**spec)
if verbose: print("memory script:", script, sep='\n')
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