Merge pull request #34 from doyle-lab-ucla/master

update dev2 to master
doyle-lab-ucla · Jun 26, 2024 · eb7658a · eb7658a
2 parents 4c5db74 + 7135aef
commit eb7658a
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/autoqchem/helper_functions.py b/autoqchem/helper_functions.py
@@ -81,10 +81,12 @@ def ssh_connect_pem(host, user, pem_path) -> fabric.Connection:
             client.connect(host,username=user,key_filename=pem_path)
         else:
             client.connect(host,username=user)
-            client.get_transport().auth_password(username=user,password=getpass.getpass(f"{user}@{host}'s password:"))
     except paramiko.ssh_exception.SSHException:
         pass
 
+    if not pem_path:
+        client.get_transport().auth_password(username=user,password=getpass.getpass(f"{user}@{host}'s password:"))
+
     c = fabric.Connection(host)
     c.client = client
     c.transport = client.get_transport()

diff --git a/autoqchem/sge_manager.py b/autoqchem/sge_manager.py
@@ -604,16 +604,16 @@ def _create_sge_file_from_gaussian_file(self, base_name, directory, wall_time) -
         output += f"# set job environment and GAUSS_SCRDIR variable\n" \
                   f". /u/local/Modules/default/init/modules.sh\n" \
                   f"module load gaussian/g16_sse4\n" \
+                  f"# another compiled version: gaussian/16_avx\n" \
                   f"export GAUSS_SCRDIR=$TMPDIR\n\n"
 
         output += f"# echo current module used to joblog\n" \
                   f"module li\n" \
                   f'echo "GAUSS_SCRDIR=$GAUSS_SCRDIR"\n' \
-                  f"# another compiled version: $g16root/16_avx/g16\n" \
-                  f"echo '/usr/bin/time -v $g16root/16_sse4/g16 < {base_name}.gjf > {base_name}.log'\n\n" \
+                  f"echo '/usr/bin/time -v $g16root/g16 < {base_name}.gjf > {base_name}.log'\n\n" \
                   f"cd {self.remote_dir}\n" \
                   f"# run command\n" \
-                  f"/usr/bin/time -v $g16root/16_sse4/g16 < {base_name}.gjf > {base_name}.log\n\n" 
+                  f"/usr/bin/time -v $g16root/g16 < {base_name}.gjf > {base_name}.log\n\n" 
 
         output += f"# echo job info to joblog\n" \
                   f"echo 'Job $JOB_ID ended on:   '' `hostname -s`\n" \