[SOLVED] analyze data from remote host

aihaike · 10-15-2008, 02:12 PM

Dear all,

I'm doing calculation on a cluster.
I order to analyze data, I wish to open output from my local machine.
For example, I'd need to do
rasmol out.xyz (out.xyz being in the cluster)

Does someone has already done such thing?
Thanks in advance,

Eric.

marozsas · 10-15-2008, 03:41 PM

uhmm...is "rasmol" a program that do the analyses on data in the remote file "out.xyz" ?
If it is, "rasmol" is a local program on your machine ? If it is, then the only remote is the data file, right ?
if it is

then you have a couple of options:
1) transfer the data file "out.xyz" from remote machine to a local directory on your machine, using ftp or scp, smbclient, etc.
2) access the remote file on a networked folder using NFS or CIFS. This could impact on the network performance depending how the file is accessed by "rasmol" - Just one read on all file is fine; it won't hurt the network performance - otherwise, several small random access will.

You could provide more info for a more precise feedback.

aihaike · 10-15-2008, 03:59 PM

Thanks for your answer.
Yes, "rasmol" is a local program on my machine, and so the only remote is the data file.
In fact. rasmol display molecule from a coordinate file *.xyz.
I thought about get back data and open them locally, but I imaged about an other possibility like
rasmol "datafile in this machine".

Actually, ssh does that but one can not use local program to open the remote file. The program needed must be installed in the remote host.

Best,

Eric.

marozsas · 10-15-2008, 04:14 PM

I see.
you can at least, simplify the remote access. I suppose "resmol" it is a program with a graphical interface running on a *nix like machine as your local computer.

Than you can not open an interactive shell on the cluster, but a "run just this command there". I mean:

Code:

user@localmachine$ ssh -X your-user-name-on-cluster@cluster-name-or-ip "rasmol out.xyz"

You got it ?

you can even create a simple alias (in fact a function if you use bash) to do that and passing the file name as argument:

Code:

function rrasmol () {
if [ "$1" = "" ]; then
                echo "Error: Argument a file name on remote cluster."
                return
fi
ssh -X your-user-name-on-cluster@cluster-name-or-ip "rasmol ${1}"
}

put this in your .alias file, source it (. .alias), and just do:

rrasmol out.xyz

If the extension of data file is constant you can even hardcode it in the alias ("rasmol ${1}.xyz") and just call "rrasmol out".

cheers,

aihaike · 10-16-2008, 04:31 AM

In fact rasmol dos not exist in the remote machine. So basically, I would need to open a remote file with a local program.
If it's not possible, I cat write a function which get the data file and open it locally.
Thanks for your help,

Eric.

aihaike · 10-18-2008, 04:47 PM

I've just discovered the powerfull sshfs.
You can mount a remote directory via ssh by simply typing:

sshfs host: local_directory/

Best,

Eric.

abolishtheun · 10-19-2008, 04:14 PM

or have someone on your IT staff set up NFS.