Workspace migration

Warning: This page originally describe the necessary steps to migrate workspaces to the new filesystems back in 2017. This page is mostly kept for documentation purposes.
Long-term, the most valuable information is the description of the utility pcp, which allows copying directory structures in parallel on Lustre filesystems. Some of the original scripts shown on this page have been modified to account for changes in the HLRS environment. The are update as fo July 2018.

User migration to new workspaces

In January 2017 the workspaces installed in 2011 with the Cray Xe6 System Hermit will be replaced. In preparation for this task, users have to migrate their workspaces onto the replacement 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.

File System	alias	mounted on
ws1	univ_1	/lustre/cray/ws1
ws2	ind_1	/lustre/cray/ws2
ws3	univ_2	/lustre/cray/ws3
ws4	res_1	/lustre/cray/ws4
ws5	ind_2	/lustre/cray/ws5
ws6	res_2	/lustre/cray/ws6

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 December 19th 2016 10:00 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 26th the “old” workspaces ws1, … ws6 will be disconnected from the Cray compute nodes. The filesystems will be available on the frontend systems for data migration until February 10th 2017.
• February 11th 2017 all data on the old filesystems will be deleted.

Operation of the workspaces will be changed:

• Due to a drop of performance on high usage of quota, no job of any group member will be scheduled for computation as long as the group quota exceeds 80%. All blocked group members get a notice by E-mail (if a valid address is registered)
• accounting
• max. lifetime of a workspace is currently 60 days
• new versions of workspace tools have got more options, please read related man pages
• users can restore expired workspaces using ws_restore
• the output of the workspace tools is slightly different

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 aprun.

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

Algorithm

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
#!/bin/bash
#PBS -N IO_copy_test
#PBS -l nodes=8
#PBS -l walltime=0:30:00
#PBS -joe

cd $PBS_O_WORKDIR

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

SOURCEDIR=<YOUR SOURCE DIRECTORY HERE>
TARGETDIR=<YOUR TARGET DIRECTORY HERE>

sleep 5 
nodes=$(qstat -f $PBS_JOBID | awk -F: '/Resource_List.nodes/ {print $1 }' | awk -F= '{print $2}')
let cores=nodes*24

/usr/bin/time -p aprun -n $cores -N24 -d1  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