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Workspace migration: Difference between revisions
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| text = This page describe the necessary steps to migrate workspaces to the new filesystems.<br/> | | text = This page describe the necessary steps to migrate workspaces to the new filesystems.<br/> | ||
End of 2021 all data on the old vulcan ws2 filesystems will be deleted. Follow the below guide to transfer your data to the new ws3 filesystems. | |||
}} | }} | ||
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On vulcan cluster a new workspace filesystem (ws3) has been integrated. The currently existing workspace file system (ws2) will be shut down by the end of the year 2021. | |||
Now, users have to migrate their workspaces located on the old filesystems onto the new filesystem. Run the command ''ws_list -a'' on a frontend system to display the path for all your workspaces, if path names match mount points in the following table, these workspaces need to | Now, users have to migrate their workspaces located on the old filesystems onto the new filesystem. Run the command ''ws_list -a'' on a frontend system to display the path for all your workspaces, if path names match mount points in the following table, these workspaces need to | ||
be migrated to the new filesystem. | be migrated to the new filesystem. | ||
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! mounted on | ! mounted on | ||
|- | |- | ||
| | | NEC_lustre | ||
| /lustre/ | | /lustre/nec/ws2 | ||
|- | |- | ||
|} | |} | ||
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== How to proceed == | == How to proceed == | ||
* from <Font color=red> | * from <Font color=red>October 4th 2021 10:00</Font> on new workspaces will be allocated on the replacement filesystem. Existing workspaces will be listed further on. | ||
* workspaces located on old filesystems can not be extended anymore. | * workspaces located on old filesystems can not be extended anymore. | ||
* if you have to migrate data from workspaces on one | * if you have to migrate data from workspaces on one to another filesystems, do not use the ''mv'' command to transfer data. For large amount of data, this will fail due to time limits. Currently we recommend for e.g. millions of small files or for large amount of data to use following command inside a single node batch job: ''rsync -a --hard-links Old_ws/ new_ws/'' | ||
* You can try to use the [[Workspace_migration#Using_mpifileutils_for_data_transfer | mpifileutils '''dcp''' or '''dsync''']] | |||
* take care when you create new batch jobs. If you have to migrate your workspace from an old filesystem to the new location, this takes time. Do not run any job while the migration process is active. This may result in inconsistent data. | * take care when you create new batch jobs. If you have to migrate your workspace from an old filesystem to the new location, this takes time. Do not run any job while the migration process is active. This may result in inconsistent data. | ||
* On <Font color=red> | * On <Font color=red>November 3rd 2021</Font> the “old” workspaces on ws2 will be disconnected from the vulcan compute nodes. The filesystems will be available on the frontend systems for some further days. | ||
* <Font color=red> | * <Font color=red>November 2021</font> all data on the old filesystems will be deleted. | ||
== Operation of the workspaces: == | == Operation of the workspaces on ws3: == | ||
* No job of any group member will be scheduled for computation as long as the group quota is exceeded. | * No job of any group member will be scheduled for computation as long as the group quota is exceeded. | ||
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* default lifetime of a workspace is 1 day | * default lifetime of a workspace is 1 day | ||
* please read related man pages or online [[Workspace_mechanism | workspace mechanism document]]<BR> | * please read related man pages or online [[Workspace_mechanism | workspace mechanism document]]<BR> | ||
: in particular note that the workspace tools allow to explicitly address a specific workspace file system using the <tt>-F</tt> option (e.g. <tt>ws_allocate -F | : in particular note that the workspace tools allow to explicitly address a specific workspace file system using the <tt>-F</tt> option (e.g. <tt>ws_allocate -F ws3 my_workspace 10</tt>) | ||
* to list your available workspace file systems use <tt>ws_list -l</tt> | * to list your available workspace file systems use <tt>ws_list -l</tt> | ||
* users can restore expired workspaces using ''ws_restore'' | * users can restore expired workspaces using ''ws_restore'' | ||
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Please read https://kb.hlrs.de/platforms/index.php/Storage_usage_policy | Please read https://kb.hlrs.de/platforms/index.php/Storage_usage_policy | ||
== Using | == Using mpifileutils for data transfer == | ||
This mpifileutils suite provides MPI-based tools to handle typical jobs like copy, remove, and compare for large datasets, providing speedups of up to 50x compared to single process jobs. It can only be run on compute nodes via mpirun. | |||
dcp or dsync is similar to cp -r or rsync; simply give it a source directory and destination and dcp / dsync will recursively copy the source directory to the destination in parallel. | |||
dcp / dsync has a number of useful options; use dcp -h or dsync -h to see a description or use the [[https://mpifileutils.readthedocs.io/en/v0.11/ User Guide]] | |||
It should be invoked via mpirun. | |||
We highly recommend to use dcp / dsync with an empty ~/.profile and ~/.bashrc only! Furthermore, take care that only the following modules are loaded when using mpifileutils (this can be achieved by logging into the system without modifying the list of modules and loading the tools/mpifileutils module only): <br> | |||
1) system/pbs/19.1.1(default) <br> | |||
2) system/batchsystem/auto <br> | |||
3) system/site_names <br> | |||
4) system/ws/1.3.5b(default) <br> | |||
5) system/wrappers/1.0(default) <br> | |||
6) mpi/ucx/1.8.1 <br> | |||
7) tools/binutils/2.32 <br> | |||
8) compiler/gnu/9.2.0(default) <br> | |||
9) mpi/openmpi/4.0.5-gnu-9.2.0(default) <br> | |||
10) tools/mpifileutils <br> | |||
=== dcp === | |||
Parallel MPI application to recursively copy files and directories. | |||
dcp is a file copy tool in the spirit of cp(1) that evenly distributes the work of scanning the directory tree, and copying file data across a large cluster without any centralized state. It is designed for copying files that are located on a distributed parallel file system, and it splits large file copies across multiple processes. | |||
Run ''' | Run '''dcp''' with the '''-p''' option to preserve permissions and timestamps, and ownership.<br> | ||
'''-p''' : preserve permissions and timestamps, and ownership | '''-p''' : preserve permissions and timestamps, and ownership | ||
'''- | '''--chunksize C''': Copy files larger than C Bytes in C Byte chunks (default ist 4MB) | ||
We highly recommend using the '''-p''' option. | |||
=== dsync === | |||
Parallel MPI application to synchronize two files or two directory trees. | |||
dsync makes DEST match SRC, adding missing entries from DEST, and updating existing entries in DEST as necessary so that SRC and DEST have identical content, ownership, timestamps, and permissions. | |||
'''--chunksize C''': Copy files larger than C Bytes in C Byte chunks (default ist 4MB) | |||
=== Job Script example === | === Job Script example === | ||
Here is an example of a job script. | Here is an example of a job script. | ||
You have to change the SOURCEDIR and TARGETDIR according to your setup. | You have to change the SOURCEDIR and TARGETDIR according to your setup. | ||
Also the number of nodes and wallclock time should be adjusted. | Also the number of nodes and wallclock time should be adjusted. | ||
#!/bin/bash | #!/bin/bash | ||
#PBS -N parallel-copy | #PBS -N parallel-copy | ||
#PBS -l select=2:mpiprocs= | #PBS -l select=2:node_type=hsw:mpiprocs=20 | ||
#PBS -l walltime=00:20:00 | #PBS -l walltime=00:20:00 | ||
module load | module load tools/mpifileutils | ||
SOURCEDIR=<YOUR SOURCE DIRECTORY HERE> | SOURCEDIR=<YOUR SOURCE DIRECTORY HERE> | ||
Line 133: | Line 117: | ||
sleep 5 | sleep 5 | ||
nodes=$(cat $PBS_NODEFILE | sort -u | wc -l) | nodes=$(cat $PBS_NODEFILE | sort -u | wc -l) | ||
let cores=nodes* | let cores=nodes*20 | ||
time_start=$(date "+%c :: %s") | time_start=$(date "+%c :: %s") | ||
mpirun -np $cores | #mpirun -np $cores dcp -p --bufsize 8MB ${SOURCEDIR}/ ${TARGETDIR}/ | ||
mpirun -np $cores dsync --bufsize 8MB $SOURCEDIR $TARGETDIR | |||
time_end=$(date "+%c :: %s") | time_end=$(date "+%c :: %s") | ||
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(( total_time=$tt_end-$tt_start )) | (( total_time=$tt_end-$tt_start )) | ||
echo "Total runtime in seconds: $total_time" | echo "Total runtime in seconds: $total_time" | ||
Revision as of 13:39, 26 April 2022
End of 2021 all data on the old vulcan ws2 filesystems will be deleted. Follow the below guide to transfer your data to the new ws3 filesystems.
User migration to new workspaces
On vulcan cluster a new workspace filesystem (ws3) has been integrated. The currently existing workspace file system (ws2) will be shut down by the end of the year 2021. Now, users have to migrate their workspaces located on the old filesystems onto the new filesystem. Run the command ws_list -a on a frontend system to display the path for all your workspaces, if path names match mount points in the following table, these workspaces need to be migrated to the new filesystem.
File System | mounted on |
---|---|
NEC_lustre | /lustre/nec/ws2 |
Before you start
Migration for large amount of data consumes a lot of IO ressources. Please review and remove data not needed any more or move it into HPSS.
How to proceed
- from October 4th 2021 10:00 on new workspaces will be allocated on the replacement filesystem. Existing workspaces will be listed further on.
- workspaces located on old filesystems can not be extended anymore.
- if you have to migrate data from workspaces on one to another filesystems, do not use the mv command to transfer data. For large amount of data, this will fail due to time limits. Currently we recommend for e.g. millions of small files or for large amount of data to use following command inside a single node batch job: rsync -a --hard-links Old_ws/ new_ws/
- You can try to use the mpifileutils dcp or dsync
- take care when you create new batch jobs. If you have to migrate your workspace from an old filesystem to the new location, this takes time. Do not run any job while the migration process is active. This may result in inconsistent data.
- On November 3rd 2021 the “old” workspaces on ws2 will be disconnected from the vulcan compute nodes. The filesystems will be available on the frontend systems for some further days.
- November 2021 all data on the old filesystems will be deleted.
Operation of the workspaces on ws3:
- No job of any group member will be scheduled for computation as long as the group quota is exceeded.
- accounting
- max. lifetime of a workspace is currently 60 days
- default lifetime of a workspace is 1 day
- please read related man pages or online workspace mechanism document
- in particular note that the workspace tools allow to explicitly address a specific workspace file system using the -F option (e.g. ws_allocate -F ws3 my_workspace 10)
- to list your available workspace file systems use ws_list -l
- users can restore expired workspaces using ws_restore
Please read https://kb.hlrs.de/platforms/index.php/Storage_usage_policy
Using mpifileutils for data transfer
This mpifileutils suite provides MPI-based tools to handle typical jobs like copy, remove, and compare for large datasets, providing speedups of up to 50x compared to single process jobs. It can only be run on compute nodes via mpirun.
dcp or dsync is similar to cp -r or rsync; simply give it a source directory and destination and dcp / dsync will recursively copy the source directory to the destination in parallel.
dcp / dsync has a number of useful options; use dcp -h or dsync -h to see a description or use the [User Guide]
It should be invoked via mpirun.
We highly recommend to use dcp / dsync with an empty ~/.profile and ~/.bashrc only! Furthermore, take care that only the following modules are loaded when using mpifileutils (this can be achieved by logging into the system without modifying the list of modules and loading the tools/mpifileutils module only):
1) system/pbs/19.1.1(default)
2) system/batchsystem/auto
3) system/site_names
4) system/ws/1.3.5b(default)
5) system/wrappers/1.0(default)
6) mpi/ucx/1.8.1
7) tools/binutils/2.32
8) compiler/gnu/9.2.0(default)
9) mpi/openmpi/4.0.5-gnu-9.2.0(default)
10) tools/mpifileutils
dcp
Parallel MPI application to recursively copy files and directories.
dcp is a file copy tool in the spirit of cp(1) that evenly distributes the work of scanning the directory tree, and copying file data across a large cluster without any centralized state. It is designed for copying files that are located on a distributed parallel file system, and it splits large file copies across multiple processes.
Run dcp with the -p option to preserve permissions and timestamps, and ownership.
-p : preserve permissions and timestamps, and ownership
--chunksize C: Copy files larger than C Bytes in C Byte chunks (default ist 4MB)
We highly recommend using the -p option.
dsync
Parallel MPI application to synchronize two files or two directory trees.
dsync makes DEST match SRC, adding missing entries from DEST, and updating existing entries in DEST as necessary so that SRC and DEST have identical content, ownership, timestamps, and permissions.
--chunksize C: Copy files larger than C Bytes in C Byte chunks (default ist 4MB)
Job Script example
Here is an example of a job script.
You have to change the SOURCEDIR and TARGETDIR according to your setup. Also the number of nodes and wallclock time should be adjusted.
#!/bin/bash #PBS -N parallel-copy #PBS -l select=2:node_type=hsw:mpiprocs=20 #PBS -l walltime=00:20:00 module load tools/mpifileutils SOURCEDIR=<YOUR SOURCE DIRECTORY HERE> TARGETDIR=<YOUR TARGET DIRECTORY HERE> sleep 5 nodes=$(cat $PBS_NODEFILE | sort -u | wc -l) let cores=nodes*20 time_start=$(date "+%c :: %s") #mpirun -np $cores dcp -p --bufsize 8MB ${SOURCEDIR}/ ${TARGETDIR}/ mpirun -np $cores dsync --bufsize 8MB $SOURCEDIR $TARGETDIR time_end=$(date "+%c :: %s") tt_start=$(echo $time_start | awk {'print $9'}) tt_end=$(echo $time_end | awk {'print $9'}) (( total_time=$tt_end-$tt_start )) echo "Total runtime in seconds: $total_time"