FAQ

Who do I contact for support

Who do I contact if I have problems or questions about how to use the SciNet systems?

Answer:

E-mail <support@scinet.utoronto.ca>

Try to avoid sending email only to specific individuals at SciNet. Your chances of a quick reply increase significantly if you email our team!

What does code scaling mean?

Answer:

Please see A Performance Primer

What do you mean by throughput?

Answer:

Please see A Performance Primer.

Here is a simple example:

Suppose you need to do 10 computations. Say each of these runs for 1 day on 8 cores, but they take "only" 18 hours on 16 cores. What is the fastest way to get all 10 computations done - as 8-core jobs or as 16-core jobs? Let us assume you have 2 nodes at your disposal. The answer, after some simple arithmetic, is that running your 10 jobs as 8-core jobs will take 5 days, whereas if you ran them as 16-core jobs it would take 7.5 days. Take your own conclusions...

MPI development and interactive testing/debugging

I am in the process of playing around with the mpi calls in my code to get it to work. I do a lot of tests and each of them takes a couple of seconds only.Sometimes (like now that I'm sending this email), all the machines are full and I'm put in the line. Since I just need a couple of SECONDS, is there any way I can test it on the log-in nodes? I can't do it using the llsubmit command and if I use mpiexec then I need a host file. Can I use a host file to run my 2 second test jobs on the log in nodes? If yes, can you send me an example host file please?

Answer:

TCS

On the TCS you can run small MPI jobs on the tcs-f11n06 node, which is meant for development use. Please don't run them on the main login node tcs-f11n05. Now, as for the hostfile, it simply looks like:

tcs-f11n06
tcs-f11n06
tcs-f11n06
tcs-f11n06

for a 4-task run. When you invoke "poe" or "mpirun", there are runtime arguments that you specify pointing to this file. You can also specify it in an environment variable MP_HOSTFILE, so, if your file is in your /scratch/USER/hostfile, then you would do

 export MP_HOSTFILE=/scratch/USER/hostfile

in your shell. You will also need to create a .rhosts file in your home director, again listing tcs-f11n06 so that poe can start jobs. After that you can simply run your program. You can use mpiexec:

 mpiexec -n 4 my_test_program

adding -hostfile /path/to/my/hostfile if you did not set the environment variable above. Alternatively, you can run it with the poe command (do a "man poe" for details), or even by just directly running it. In this case the number of MPI processes will by default be the number of entries in your hostfile.

GPC

On the GPC one can run short test jobs on the GPC development nodes . Even better, though, is to request an interactive job and run the tests either in regular batch queue or using a shorter high availability debug queue.

How can I monitor my jobs on TCS?

By the way, how can I monitor the load? not with llq?

Answer:

You can get more information with the command

/xcat/tools/tcs-scripts/LL/jobState.sh

which I alias as:

alias llq1='/xcat/tools/tcs-scripts/LL/jobState.sh'

If you run "llq1 -n" you will see a listing of jobs together with a lot of information, including the load.

Autoparallelization does not work!

I compiled my code with the -qsmp=omp,auto option, and then I specified that it should be run with 64 threads - with

export OMP_NUM_THREADS=64

However, when I check the load using llq1 -n, it shows a load on the node of 1.37. Why?

Answer:

Using the autoparallelization will only get you so far. In fact, it usually does not do too much. What is helpful is to run the compiler with the -qreport option, and then read the output listing carefully to see where the compiler thought it could parallelize, where it could not, and the reasons for this. Then you can go back to your code and carefully try to address each of the issues brought up by the compiler. We emphasize that this is just a rough first guide, and that the compilers are still not magical!

Another transport will be used instead

I get error messages like the following when running on the GPC at the start of the run, although the job seems to proceed OK. Is this a problem?

--------------------------------------------------------------------------
[[45588,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: gpc-f101n005

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------

Answer:

Everything's fine. The two MPI libraries scinet provides work for both the InifiniBand and the Gigabit Ethernet interconnects, and will always try to use the fastest interconnect available. In this case, you ran on normal gigabit GPC nodes with no infiniband; but the MPI libraries have no way of knowing this, and try the infiniband first anyway. This is just a harmless `failover' message; it tried to use the infiniband, which doesn't exist on this node, then fell back on using Gigabit ethernet (`another transport').

OpenMP on the TCS

How do I run an OpenMP job on the TCS?

Answer:

Please look at the TCS Quickstart page.

I changed my .bashrc/.bash_profile and now nothing works

The default startup scripts provided by SciNet are as follows. Certain things - like sourcing /etc/profile and /etc/bashrc are required for various SciNet routines to work!

.bash_profile <source lang="bash"> if [ -f /etc/profile ]; then

      . /etc/profile

fi

1. commands which work for both GPC and TCS can go here

alias passwd='echo "Please use the SciNet portal to change password: https://portal.scinet.utoronto.ca/change_password"'

HOST=$(uname)

if [ "${HOST}" == "AIX" ] then

       # do things for the TCS machine
       alias llq1='/xcat/tools/tcs-scripts/LL/jobState.sh'
       alias llstat='/xcat/tools/tcs-scripts/LL/jobSummary.sh'

       if [ "${TERM}" = "xterm-color" ]; then
               export TERM=xterm
       fi

       # user environment for login shells goes here
       # replace colon with your own commands
       :

else

       # do things for the GPC machine
       # user environment for login shells goes here
       # replace colon with your own commands
       :

fi

PS1="\h-\$ "

if [ -f ~/.bashrc ]; then

      . ~/.bashrc

fi </source>

.bashrc <source lang="bash"> if [ -f /etc/bashrc ]; then

      . /etc/bashrc

fi

1. commands which work for both GPC and TCS can go here

HOST=$(uname)

if [ "${HOST}" == "AIX" ]; then

       # do things for the TCS machine
       # user environment for all shells goes here
       # replace colon with your own commands
       :

else

       # do things for the GPC machine

       module load intel openmpi

       # user environment for all shells goes here
       # replace colon with your own commands
       :

fi </source>

How do I run serial jobs on GPC?

Answer:

So it should be said first that SciNet is a parallel computing resource, and our priority will always be parallel jobs. Having said that, if you can make efficient use of the resources using serial jobs and get good science done, that's good too, and we're happy to help you.

The GPC nodes each have 8 processing cores, and making efficient use of these nodes means using all eight cores. As a result, we'd like to have the users take up whole nodes (eg, run multiples of 8 jobs) at a time. The most straightforward way to do this is to bunch the jobs in groups of 8 that will take roughly the same amount of time, and create a job that looks a bit like this

<source lang="bash">

1. !/bin/bash
2. MOAB/Torque submission script for multiple serial jobs on
3. SciNet GPC
5. PBS -l nodes=1:ppn=8,walltime=1:00:00
6. PBS -N serialx8

1. DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from

cd $PBS_O_WORKDIR

1. EXECUTION COMMAND; ampersand off 8 jobs and wait

(cd jobdir1; ./dojob1) & (cd jobdir2; ./dojob2) & (cd jobdir3; ./dojob3) & (cd jobdir4; ./dojob4) & (cd jobdir5; ./dojob5) & (cd jobdir6; ./dojob6) & (cd jobdir7; ./dojob7) & (cd jobdir8; ./dojob8) & wait </source>

There are three important things to take note of here. First, the wait command at the end is crucial; without it the job will terminate immediately, killing the 8 programs you just started.

Second is that it is important to group the programs by how long they will take. If (say) dojob8 takes 2 hours and the rest only take 1, then for one hour 7 of the 8 cores on the GPC node are wasted; they are sitting idle but are unavailable for other users, and the utilization of this node over the whole run is only 56%. This is the sort of thing we'll notice, and users who don't make efficient use of the machine will have their ability to use scinet resources reduced.

Third is that it is necessary to have a good idea of how much memory the jobs will require. The GPC compute nodes have about 14.5GB in total available to user jobs running on the 8 cores (a bit less, say 13GB, on the devel ndoes gpc01..04). So the jobs also have to be bunched in ways that will fit into 14.5GB. If that's not possible -- each individual job requires significantly in excess of ~1.8GB -- then its possible in principle to just run fewer jobs so that they do fit; but then, again there is an under-utilization problem. In that case, the jobs are likely candidates for parallelization, and you can contact us at <support@scinet.utoronto.ca> and arrange a meeting with one of the technical analysts to help you do just that.

How do I run serial jobs on TCS?

Answer: You don't.

On GPC, `Job cannot be executed'

I get error messages like this trying to run on GPC:

PBS Job Id: 30414.gpc-sched
Job Name:   namd
Exec host:  gpc-f120n011/7+gpc-f120n011/6+gpc-f120n011/5+gpc-f120n011/4+gpc-f120n011/3+gpc-f120n011/2+gpc-f120n011/1+gpc-f120n011/0
Aborted by PBS Server 
Job cannot be executed
See Administrator for help



PBS Job Id: 30414.gpc-sched
Job Name:   namd
Exec host:  gpc-f120n011/7+gpc-f120n011/6+gpc-f120n011/5+gpc-f120n011/4+gpc-f120n011/3+gpc-f120n011/2+gpc-f120n011/1+gpc-f120n011/0
An error has occurred processing your job, see below.
request to copy stageout files failed on node 'gpc-f120n011/7+gpc-f120n011/6+gpc-f120n011/5+gpc-f120n011/4+gpc-f120n011/3+gpc-f120n011/2+gpc-f120n011/1+gpc-f120n011/0' for job 30414.gpc-sched

Unable to copy file 30414.gpc-sched.OU to cmadill@gpc-f101n084.scinet.local:/scratch/cmadill/projects/sim-performance-test/runtime/l/namd/8/namd.o30414
*** error from copy
30414.gpc-sched.OU: No such file or directory
*** end error output

Try doing the following:

mkdir /scratch/${USER}/.pbs_spool
ln -s /scratch/${USER}/.pbs_spool ~/.pbs_spool

This is how all new accounts are setup on SciNet.

/home on GPC for compute jobs is mounted as a read-only file system. PBS by default tries to spool its output files to ${HOME}/.pbs_spool which fails as it tries to write to a read-only file system. New accounts at SciNet get around this by having ${HOME}/.pbs_spool point to somewhere appropriate on /scratch, but if you've deleted that link or directory, or had an old account, you will see errors like the above.

Why hasn't my job started?

Answer:

Use the moab command

checkjob -v jobid

and the last couple of lines should explain why a job hasn't started.

Please see Job Scheduling System (Moab) for more detailed information

How do I figure out when my job will run?

Answer:

Please see Job Scheduling System (Moab)

How do I find out my disk usage?

Answer:

The standard unix/linux utilities for finding the amount of disk space used by a directory are very slow, and notoriously inefficient on the GPFS filesystems that we run on the SciNet systems. There are utilities that very quickly report your disk usage:

The

mmlsquota

command lists the user's current usage on the filesystems that run quotas (currently /home).

In order to get the usage on the /scratch filesystem, run the command

/scinet/gpc/bin/scratchUsage

In addition, the diskUsage command, available on the login nodes and the GPC devel nodes, reports how much disk space is being used by yourself and your group on the home, scratch, and project file systems, and how much remains available. This information is updated hourly. More information about these filesystems is available at the Storage Quick-start.

How do we manage job priorities within our research group?

Answer:

Obviously, managing shared resources within a large group - whether it is conference funding or CPU time - takes some doing.

It's important to note that the fairshare periods are intentionally kept quite short - just two weeks long. (These exact numbers subject to change as the year goes on and we better understand use patterns, but they're unlikely to change radically). So, for example, let us say that in your resource allocation you have about 10% of the machine. Then for someone to use up the whole two week amount of time in 2 days, they'd have to use 70% of the machine in those two days - which is unlikely to happen by accident. If that does happen, those using the same allocation as the person who used 70% of the machine over the two days will suffer by having much lower priority for their jobs, but only for the next 12 days - and even then, if there are idle cpus they'll still be able to compute.

There will be online tools for seeing how the allocation is being used, and those people who are in charge in your group will be able to use that information to manage the users, telling them to dial it down or up. We know that managing a large research group is hard, and we want to make sure we provide you the information you need to do your job effectively.

How can I automatically resubmit a job?

Commonly you may have a job that you know will take longer to run than what is permissible in the queue. As long as your program contains checkpoint or restart capability, you can have one job automatically submit the next. In the following example it is assumed that the program finishes before the 48 hour limit and then resubmits itself by logging into one of the development nodes.

<source lang="bash">

1. !/bin/bash
2. MOAB/Torque example submission script for auto resubmission
3. SciNet GPC
5. PBS -l nodes=1:ppn=8,walltime=48:00:00
6. PBS -N my_job

1. DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from

cd $PBS_O_WORKDIR

1. YOUR CODE HERE

./run_my_code

1. RESUBMIT 10 TIMES HERE

num=$NUM if [ $num -lt 10 ]; then

     num=$(($num+1))
     ssh gpc01 "cd $PBS_O_WORKDIR; qsub ./script_name.sh -v NUM=$num";

fi </source>

qsub script_name.sh -v NUM=1

How can I pass in arguments to my submission script?

If you wish to make your scripts more generic you can use qsub's ability to pass in environment variables to pass in arguments to your script. The following example shows a case where an input and an output file are passed in on the qsub line. Multiple variables can be passed in using the qsub "-v" option and comma delimited.

<source lang="bash">

1. !/bin/bash
2. MOAB/Torque example of passing in arguments
3. SciNet GPC
5. PBS -l nodes=1:ppn=8,walltime=48:00:00
6. PBS -N my_job

1. DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from

cd $PBS_O_WORKDIR

1. YOUR CODE HERE

./run_my_code -f $INFILE -o $OUTFILE </source>

qsub script_name.sh -v INFILE=input.txt,OUTFILE=outfile.txt

How do I transfer data to/from SciNet?

Answer:

All incoming connections to SciNet go through relatively low-speed connections to the login.scinet gateways, so using scp to copy files the same way you ssh in is not an effective way to move lots of data. Better tools are described in our page on Data Transfer.

How can I check if I have files in /scratch that are scheduled for automatic deletion?

Answer:

Please see Storage At SciNet

How can I run Matlab / IDL / my favourite commercial software on SciNet?

Answer:

Because SciNet serves such a disparate group of user communities, there is just no way we can buy licenses for everyone's commercial package. The only commercial software we have purchased is that which in principle can benefit everyone -- fast compilers and math libraries (Intel's on GPC, and IBM's on TCS).

If your research group requires a commercial package that you already have or are willing to buy licenses for, contact us at support@scinet and we can work together to find out if it is feasible to implement the packages licensing arrangement on the SciNet clusters, and if so, what is the the best way to do it.

Note that it is important that you contact us before installing commercially licensed software on SciNet machines, even if you have a way to do it in your own directory without requiring sysadmin intervention. It puts us in a very awkward position if someone is found to be running unlicensed or invalidly licensed software on our systems, so we need to be aware of what is being installed where.

Next question, please

Send your question to <support@scinet.utoronto.ca>; we'll answer it asap!