We have added SSDs, solid state disks, on a few compute nodes:
- These are local fast disks that can speed up applications that preform a lot of intensive I/O operations,
- hence such jobs should complete faster when using SSDs.
- Jobs that do not perform intensive I/Os should not use the SSDs - these are this is a scarce shared resource.
- Since these disks are local to the compute nodes:
- you cannot see the SSD from either login nodes,
- your job will be able to use the SSD only while the job is running, hence
- you need to prepare the files needed for a job prior to submitting the job, using /pool or /scratch, and
request the right amount of SSD disk space:
this is the maximum amount of disk space your job will need on the SSD at run-time, (similarly to the maximum of memory it will need).
- Your job script will have to
- copy those files to the SSD before processing them,
- adapted be adjusted to use the SSD,
- upon completion, copy the results from the SSD elsewhere (/pool or /scratch), and
- and delete what you wrote on the SSD.
- If you exceed the amount of disk space, i.e., your quota, your job won't be able to write any longer to the SSD,
hence your job script should stop when encountering such error.
Since you can't access the SSDs from a login node, you must prepare the data the job will need somewhere else, like on
/pool (or on
/scratch) before submitting a job.
Remember, your job will still be able to access the
/home, /data, /pool, and
/scratch disks, hence you don't have to copy everything on the SSD,
only the I/O intensive part of the analysis should use the SSD.
How to Prepare my Data
- Create a subdirectory in
/scratch)and move or copy the data you will need, for example (as user smart1)
mkdir -p great/project/wild-cat
Now is have a directory for this case, and would copy the I/O intensive part of the required data set in it.
- While not required, you can pack these data in a compressed tar-ball
tar cfz ../wild-cat.tgz .
/pool/genomics/smart1/great/project/wild-cat.tgznow holds you input data set,
being compressed it is likely to be smaller than the content of
That directory can be deleted, unless you will need it later.
- Ancillary data and/or configuration files that are not causing intensive I/O can stay on a location under
How to Adjust
a Job Script to Use the SSD
Your jobs script will need the following 4 parts
Part 1: Copy the Data to the SSD
- At the top of your job script, load the
tools/ssdmodule and copy or extract your data set as follows:
- At the top of your job script, load the
The advantage of the compressed tar-ball is that the
.tgz file is likely to be smaller than the content of the directory, hence less I/O transfer from the
/pool disk, while un-compressing and writing to the SSD is fast,
Part 2: Adjust the Script or a Configuration File
- You need to replace all references to
- this can be easily done at the shell script level, but not in a configuration file, i.e., for flags/options
execute -o /pool/genomics/smart1/great/project/wild-cat/result.dat
is replaced by
execute -o $SSD_DIR/result.dat
- Here is a simple trick to modify a configuration file:
Let's assume that your analysis uses a file
wow.conf, where for instance the full path of some files must be listed, like:
Code Block language bash title wow.conf
# this is the configuration file of the fabulous WOW package input=/pool/genomics/smart1/great/project/wild-cat/wiskers.dat output=/pool/genomics/smart1/great/project/wild-cat/tail.dat paws=4 eyes=2
wow.conffile by a
wow.genfile as follows:
Code Block language bash title wow.gen
# this is the configuration file of the fabulous WOW package input=XXXX/wiskers.dat output=XXXX/wild-cat/tail.dat paws=4 eyes=2
And create thethe
wow.confconffile from thethe
wow.gengenat run-time by adding the following in the job script:
Code Block language bash
sed "s=XXXX=$SSD_DIR=" wow.gen > wow.conf
As long as
XXXXis not used for anything else, this will replace every occurrence of
XXXXby the value of the environment variablevariable
Part 3: Run the Analysis
- With your data copied to the SSD and with your commands and configuration files adjusted to use the SSD, run your analysis.
Part 4: Copy the Results from the SSD
At the end of the job script, you must add instruction instructions to copy the results of your analysis back to
If/when the results are easily identifiable, you can use
the commands mv
find, here are a few examples:
Move the directory where all the results are stored and the log file, delete the rest.
Code Block language bash title moving identifiable results, delete the rest
# move results and log file back cd $SSD_DIR mv results /pool/genomics/smart1/great/project/wild-cat/. mv wow.log /pool/genomics/smart1/great/project/wild-cat/. # # delete the rest rm -rf *
Move the directory where all the results are stored and the log file, delete the input (conservative approach, in case you missed something).
Code Block language bash title moving identifiable results, delete known input sets
# move results and log file back cd $SSD_DIR mv results /pool/genomics/smart1/great/project/wild-cat/. mv wow.log /pool/genomics/smart1/great/project/wild-cat/. # # delete input set and other stuff rm -rf input rm wow.gen wow.conf
Move using the
Code Block language bash title moving using --update
# move results using --update cd $SSD_DIR mv --update * /pool/genomics/smart1/great/project/wild-cat/. # # delete the rest rm -rf *
Note, you can use
mv --updateon an explicit list (of files, directories, or file specification), not just * (everything), and you do not have to remove the rest, but can only remove what you know you can safely remove (conservative approach).
Find newer files and move them: the trick is to create a 'timestamp' file before starting the analysis.
That file can be used later to find any newer file with the
Code Block language bash title Using a timestamp file and tar --newer=
# set the timestamp date > $SSD_DIR/started.txt # run the analysis ... # copy the new files in the subdir data/ to a compressed tar-ball cd $SSD_DIR tar --newer=$SSD_DIR/started.txt -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz data/ # now remove it rm -rf data/ # etc... # delete everything, unless rm -rf *
See previous comments and what to tar and what to remove: once you've
tar'd new stuff in
Using the timestamp file and the
Code Block language bash title Using find and a timestamp file
# set the timestamp date > $SSD_DIR/started.txt # run the analysis ... # find the new files in the subdir data/ cd $SSD_DIR find data/ -newer $SSD_DIR/started.txt -type f > /tmp/list # do the same on logs/, append to the list find logs/ -newer $SSD_DIR/started.txt -type f >> /tmp/list # etc... # now save what is in the list with one tar tar --files-from=/tmp/list -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz data/ # now remove data/ and logs/ rm -rf data/ logs/ # etc... # delete everything, unless rm -rf *
There are many more ways to accomplish this ....
BTW, the advantage of writing a
.tgzfile, rather than moving files is two fold, assuming your stuff is compressible: There are many more ways to accomplish this ....
You write less in the .tgz file, so it should be done faster (reading and compressing should be fast, writing is the slow step)
you need less disk space for your output (since it is compressed).
The drawback being that you need to know how to handle/view/deal with a
A Pseudo Example
Here is what a job script might look like:
# #$ -N example #$ -o example.log -cwd -j y #$ -q uTxlM.rq #$ -l ssduse=2560G,hm,mres=20G,h_data=20G,h_vmem=20G # # pseudo example using a fake package WOW, on the SSD # echo $JOB_NAME started `date` on $HOSTNAME in $QUEUE jobID=$JOB_ID # module load tools/ssd module load special/wow # # create a wow config file from a generic version, to insert the SSD temp dir value sed "s=XXXX=$SSD_DIR=" ~/wow/wild-cat.gen > ~/wow/wild-cat.conf # # cd to the SSD temp dir and copy the data set to it, using the existing .tgz file cd $SSD_DIR tar xf /pool/genomics/smart1/great/project/wild-cat.tgz # # create some sub dirs for output and logs mkdir output mkdir logs # # run the wow analysis (note how some files are not on the SSD) wow --type=m --params=$HOME/wow/parameters.dat --config=$HOME/wow/wild-cat.conf -o $SSD_DIR/output -l $SSD_DIR/logs # # save the output and the logs in a tar compressed file # (assumes wow did not change current working directory) # otherwise insert: cd $SSD_DIR tar -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz output/ logs/ # # remove everything (in $SSD_DIR), or remove what you know you can (conservative option) rm -rf * # echo $JOB_NAME done `date`
Usage Monitoring Tools
- We have two tools to monitor SSD usage, one on a per-job basis, and one to view usage summary.
- Both need you to load the
Per Job Basis
% module load tools/local % module load gnuplot % plot-qssduse.pl -x 7420073
This example plots the SSD usage of job 7420073 to the screen, assuming you have an X-windows capable connection,
- drop the
-xto plot to a file,
- and use
NNNN.TTT, instead of
NNNNto show usage for a given task (
TTT) of a job array (
man plot-qssduse.plfor more information.
% module load tools/local % module load gnuplot % plot-qssduse-summary.pl -x
- drop the
-xto plot to a file.
man plot-qssduse-summary.plfor more information.
Last Updated SGK