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Difference between revisions of "Workspace migration"

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Line 120: Line 120:
  #PBS -N IO_copy_test
  #PBS -N IO_copy_test
  #PBS -l nodes=8
  #PBS -l select=8:mpiprocs=128:node_type=rome
  #PBS -l walltime=0:30:00
  #PBS -l walltime=0:30:00
  #PBS -joe
  #PBS -joe
Line 135: Line 135:
  sleep 5  
  sleep 5  
  nodes=$(qstat -f $PBS_JOBID | awk -F: '/Resource_List.nodes/ {print $1 }' | awk -F= '{print $2}')
  nodes=$(cat $PBS_NODEFILE | sort -u | wc -l)
  let cores=nodes*24
  let cores=nodes*128
  /usr/bin/time -p mpirun -n $cores -N24 -d1 pcp -l -ls 1048576  -b 4096 $SOURCEDIR $TARGETDIR
  /usr/bin/time -p mpirun -n $cores -N128 pcp -l -ls 1048576  -b 4096 $SOURCEDIR $TARGETDIR

Revision as of 16:24, 4 November 2020

User migration to new workspaces

With the installation of HPE Apollo 9000 (Hawk) a new fast workspace filesystem was integrated. For a certain transition period the workspace filesystem of the predecessor system Cray XC40 hazelhen (Sonexion ws9) was integrated at the same time. Now, users have to migrate their workspaces located on the old filesystem onto the new filesystems. 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
ws9.0 /lustre/cray/ws9/0
ws9.1 /lustre/cray/ws9/1
ws9.2 /lustre/cray/ws9/2
ws9.3 /lustre/cray/ws9/3
ws9.4 /lustre/cray/ws9/4
ws9.5 /lustre/cray/ws9/5
ws9.6 /lustre/cray/ws9/6
ws9.6p /lustre/cray/ws9/6

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 NovDecember XXth 2020 X0:00 on new workspaces will be allocated on the replacement filesystems. 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 of the above listed filesystems, do not use the mv command to transfer data. For large amount of data, this will fail due to time limits. We recommend using parallel copy programm pcp for large amount of data in large files. If this fails for e.g. millions of small files following command may help: rsync -a --hard-links Old_ws/ new_ws/
  • 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 January 31th 2021 the “old” workspaces ws9.* will be disconnected from the HPE Apollo 9000 compute nodes. The filesystems will be available on the frontend systems for data migration until February 14th 2021.
  • February 15th 2021 all data on the old filesystems will be deleted.

Operation of the workspaces:

  • 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 ws14.1 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 a parallel copy for data transfer

pcp is a python based parallel copy using MPI. It can only be run on compute nodes via mpirun.

pcp is similar to cp -r; simply give it a source directory and destination and pcp will recursively copy the source directory to the destination in parallel.

pcp has a number of useful options; use pcp -h to see a description.

This program traverses a directory tree and copies files in the tree in parallel. It does not copy individual files in parallel. It should be invoked via aprun.

Basic arguments

If run with the -l flag or -lf flags pcp will be stripe aware.

-l will cause stripe information to be copied from the source files and directories.

-lf will cause all files and directories on the destination to be striped, regardless of the striping on the source.

Striping behavior can be further modified with -ls and -ld.

-ls will set a minimum file size. Files below this size will not be striped, regardless of the source striping.

-ld will cause all directories to be unstriped.

-b C: Copy files larger than C Mbytes in C Mbyte chunks


pcp runs in two phases:

Phase I is a parallel walk of the file tree, involving all MPI ranks in a peer-to-peer algorithm. The walk constructs the list of files to be copied and creates the destination directory hierarchy.

In phase II, the actual files are copied. Phase II uses a master-slave algorithm. R0 is the master and dispatches file copy instructions to the slaves (R1...Rn).

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.

Again, pcp does NOT parallelize a single copy operation, but the number of copy operations are distributed over the nodes.

> cat pcp.qsub
#PBS -N IO_copy_test
#PBS -l select=8:mpiprocs=128:node_type=rome
#PBS -l walltime=0:30:00
#PBS -joe


# originally:
# module load tools/python/2.7.8
# currently:
module load python-site/2.7


sleep 5 
nodes=$(cat $PBS_NODEFILE | sort -u | wc -l)
let cores=nodes*128

/usr/bin/time -p mpirun -n $cores -N128  pcp -l -ls 1048576  -b 4096 $SOURCEDIR $TARGETDIR

Output of a run with the script

R0: All workers have reported in.
Starting 192 processes.
Will copy lustre stripe information.
Files larger than 4096 Mbytes will be copied in parallel chunks.
Will not stripe files smaller than 1.00 Mbytes 

Starting phase I: Scanning and copying directory structure...
Phase I done: Scanned 115532 files, 1007 dirs in 00 hrs 00 mins 01 secs (106900 items/sec).
115532 files will be copied.

Starting phase II: Copying files...
Phase II done.

Copy Statisics:
Rank 1 copied 7.00 Gbytes in 839 files (38.17 Mbytes/s)
Rank 2 copied 6.37 Gbytes in 825 files (34.75 Mbytes/s)
Rank 190 copied 7.84 Gbytes in 495 files (42.78 Mbytes/s)
Rank 191 copied 7.25 Gbytes in 784 files (39.63 Mbytes/s)
Total data copied: 1.47 Tbytes in 115606 files (7.09 Gbytes/s)
Total Time for copy: 00 hrs 03 mins 31 secs
Warnings 0
Application 6324961 resources: utime ~4257s, stime ~4005s, Rss ~33000, inblocks ~3148863732, outblocks ~3148201243
real 259.90
user 0.02
sys 0.01