In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
!!! Note "Note"
Consider preloading inputs and executables onto [shared scratch](../storage/storage/) before the calculation starts.
Consider preloading inputs and executables onto [shared scratch](storage/) before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
...
...
@@ -382,7 +382,7 @@ sections.
!!! Note "Note"
Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.
Example jobscript for single node calculation, using [local scratch](../storage/storage/) on the node:
Example jobscript for single node calculation, using [local scratch](storage/) on the node:
@@ -55,7 +55,7 @@ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
Example to the cluster login:
!!! Note "Note"
The environment is **not** shared between login nodes, except for [shared filesystems](../anselm-cluster-documentation/storage/storage/#shared-filesystems).
The environment is **not** shared between login nodes, except for [shared filesystems](storage/#shared-filesystems).
Data Transfer
-------------
...
...
@@ -114,7 +114,7 @@ $ man sshfs
On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Anselm filesystems directly as an external disc.
More information about the shared file systems is available [here](../anselm-cluster-documentation/storage/storage/).
More information about the shared file systems is available [here](storage/).
In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
!!! Note "Note"
Consider preloading inputs and executables onto [shared scratch](../storage/storage/) before the calculation starts.
Consider preloading inputs and executables onto [shared scratch](storage/) before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
...
...
@@ -441,7 +441,7 @@ HTML commented section #2 (examples need to be reworked)
!!! Note "Note"
Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory.
Example jobscript for single node calculation, using [local scratch](../storage/storage/) on the node:
Example jobscript for single node calculation, using [local scratch](storage/) on the node:
@@ -42,7 +42,7 @@ On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/access
After logging in, you will see the command prompt:
!!! Note "Note"
The environment is **not** shared between login nodes, except for [shared filesystems](../salomon/storage/storage/).
The environment is **not** shared between login nodes, except for [shared filesystems](storage/).
Data Transfer
-------------
...
...
@@ -92,7 +92,7 @@ $ man sshfs
On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available [here](../salomon/storage/storage/).
More information about the shared file systems is available [here](storage/).
