I was trying to configure a remote server for IQmol for teaching a quantum chemistry class. I tried two clusters and got different problems. For both clusters I chose “SSH” as the connection method and “password” as the authentication method.
(a) For the first cluster, the password prompt showed up and IQmol was actually able to connect to that cluster. The working directory was successfully created there by IQmol. However, the job then failed to start after that, with the error message below:
Job submission failed
Unable to open remote file handle with SFTP
$HOME/IQmol/IQmol.inp
(b) For the 2nd one, IQmol was unable to connect. When I hit submit, a message which seemed incomplete showed up:
Host not found in
Add host to file?
I thought this is trying to edit the ~/.ssh/known_hosts file. But then an error message showed up:
Failed to connnect to server xxxx
Unable to write to file
It is strange to me that the two clusters had different behaviors. The only difference I can think of is the 2nd server requires our campus VPN to login, which I did turn on when I was using IQmol.
I was wondering if it is possible to get either of these work. Thanks!
Update: I got the former one working by explicitly spelling out the working directory /home/ymao/IQmol. “$HOME” seems to be causing trouble
For the 2nd cluster, I found that when configuring SSH, I need to replace $HOME/.ssh/known_hosts to something customized, like $HOME/.iqmol_hosts, then the password prompt will show up as in the first one.
However, I was unable to fully resolve the problem for the 2nd cluster: while IQmol server copied the input and created the run script on the server, it didn’t actually run the calculation and passed it back without reporting any errors. I don’t know what has stopped the remote server from executing the run script.
You are correct, environment variables do cause problems. I have added a note to this effect in the server configuration dialog.
As for the second server, when you submit the job, you do not have to give the full path, just the sub directory name. The working directory specified in the server setup will be prepended to this subdirectory and I am not sure if this is causing a problem. You should try submitting the job specifying only the subdirectory name.
Also, does the ch4_mac2.inp_1368429.0 file get generated when you submit the job via IQmol? If so, do the contents give any clues on why the job does not run?
Thanks Andrew. Specifying the working directory during server setup is definitely a better way of doing it.
The ch4_mac2.inp_1368429.0 file is generated when submitting the job via IQmol and its content is simply a copy of the input file. One interesting thing I just noticed: If I source the script to set up my own developer q-chem instead of the release version in the run script and do the submission in the same way, an output can be produced correctly.
I then really don’t understand why the same doesn’t work for the Q-Chem release.