diff --git a/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md b/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md index 4f91a18ea914db14f5398bad2b478d365d072d8c..3d3bb34e62130c48205c35956ac487c80aee8055 100644 --- a/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md +++ b/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md @@ -342,7 +342,7 @@ exit 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: ```bash #!/bin/bash diff --git a/docs.it4i/anselm-cluster-documentation/prace.md b/docs.it4i/anselm-cluster-documentation/prace.md index 0609a6d97a68ea316798e3a22a25903be98d13fc..d8699bf6e7487f5ce48315b8226974ae0e2191a5 100644 --- a/docs.it4i/anselm-cluster-documentation/prace.md +++ b/docs.it4i/anselm-cluster-documentation/prace.md @@ -197,7 +197,7 @@ Generally both shared file systems are available through GridFTP: |/home|Lustre|Default HOME directories of users in format /home/prace/login/| |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster| -More information about the shared file systems is available [here](storage/storage/). +More information about the shared file systems is available [here](storage/). Usage of the cluster -------------------- diff --git a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md b/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md index 3a21bd2d750e76aa454eed7d93d9fb67f6266b5d..3c85a42c51c75e7e4d832f53a129806736997dd4 100644 --- a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md +++ b/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md @@ -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/). Connection restrictions diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md index 4be50e35c11cd0f6ce1c1718ccdf8827ec186e61..9738861315dadced3de4f71a1901c3765ee67bbd 100644 --- a/docs.it4i/salomon/job-submission-and-execution.md +++ b/docs.it4i/salomon/job-submission-and-execution.md @@ -402,7 +402,7 @@ exit 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: ```bash #!/bin/bash diff --git a/docs.it4i/salomon/shell-and-data-access.md b/docs.it4i/salomon/shell-and-data-access.md index 11349f37feb6f6f947332674592c723dbbc9c668..28cce625d6d59e81ff1f51f706a6d24801c6774f 100644 --- a/docs.it4i/salomon/shell-and-data-access.md +++ b/docs.it4i/salomon/shell-and-data-access.md @@ -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/). Connection restrictions -----------------------