Author: Andy Ohlin

Inorganic chemist with an interest in geochemistry and the world around us.

Microsoft Exchange at UMU on Thunderbird on Linux

NOTE: this may not work if you have a student email address at UmU.

You’ll need to install two add-ons:

  • Lightning — install this via Tools/Add-ons in Thunderbird
  • Exchange EWS Provider — download the .xpi file from here: https://github.com/Ericsson/exchangecalendar/releases, then go to Tools/Add-ons, click the cog-wheel in the upper right corner, next to the search box, and select “Install Add-on from file”

Now to go to Events and Tasks/Calendar in Thunderbird, go to File/New/Calendar, pick On the Network, Next. Pick Microsoft Exchange, Next. Call it whatever you want, and pick the email address associated with it (your UMU email).

Selected Hosted Exchange, Use Exchange’s autodiscovery function, and click Perform autodiscovery. Select https://webmail.ad.umu.se/EWS/Exchange.asmx

Put your CAS ID (along the lines of abcd01234) in the Username box, and click on Check Server and Mailbox

Then click Next. Done!

 

Modifying ECCE to work with SLURM

In the ECCE file apps/siteconfig/QueueManagers, add

#
QueueManagers:      LoadLeveler \
            Maui \
            EASY \
            PBS \
            LSF \
            Moab \
            SGE \
            Shell\
            Slurm

#

and add this to the end of the file:

###############################################################################
# SLURM
# Simple Linux Utility for Resource Management
#
#
Slurm|submitCommand:           sbatch ##script##
Slurm|cancelCommand:           scancel ##id##
Slurm|queryJobCommand:         squeue
Slurm|queryMachineCommand:     sinfo -p ##queue##
Slurm|queryQueueCommand:       squeue -a
Slurm|queryDiskUsageCommand:   df -k
Slurm|jobIdParseExpression:    .*
Slurm|jobIdParseLeadingText:   job

Also, edit apps/scripts/eccejobmonitor and add (without line numers):

2124 LogMsg "Globus status from eccejobstore: $state";
2125 }
2126 elsif ($q eq 'slurm') 
2127 {
2128 $cmd = "squeue 2>&1";
2129 if (open(QUERY, "$cmd |"))
2130 {
2131 $gotState = 0;
2132 while ()
2133 { 
2134 LogMsg "JobCheck: Slurm qstat line: $_";
2135 if (/^\s*$id/)
2136 {
2137 my $state = (split)[5];
2138 
2139 &MsgSendUp("Slurm job id '$id' in state '$state'");
2140 
2141 if (grep {$state eq $_} qw{R
2142 t})
2143 {
2144 $status = $JOB_STATE_RUNNING;
2145 }
2146 elsif (grep {$state eq $_} qw{PD})
2147 {
2148 $status = $JOB_STATE_PENDING;
2149 }
2150 $gotState = 1;
2151 last;
2152 }
2153 }
2154 if ($gotState == 0)
2155 { 
2156 if ($gJobCheckState != $JOB_STATE_NONE)
2157 {
2158 $status = $JOB_STATE_DONE;
2159 }
2160 }
2161 close QUERY;

Now when you’re adding or modifying a machine with ecce -admin you can select Slurm. You’ll still need to edit your CONFIG.xxxx file after the machine creation and add account information etc.

 

Kebnekaise/HPC2N with ECCE at UMU

You’ll need to have modified ECCE to work with SLURM first. That’s a separate post.

Make sure to run your jobs in /pfs/nobackup/home/X/Username and use /scratch for /scratch

Once you’ve got ECCE modified for SLURM, this is what goes into your CONFIG.kebnekaise file under apps/siteconfig/

NWChem: /lap/nwchem/6.5/bin/nwchem
Gaussian-03: /hpc2n/eb/software/Core/gaussian/16.A.03-SSE4/g16
perlPath: /usr/local/bin/
qmgrPath: /usr/local/bin/
xappsPath: /usr/local/bin/
Slurm {
#!/bin/bash
#SBATCH -A SNIC2017-X-Y
#SBATCH -c $totalprocs
#SBATCH -n 1
#SBATCH --time=$walltime
#SBATCH --output=job.%J.out
#SBATCH --error=job.%J.err
#SBATCH --job-name=$submitFile
}
Gaussian-03FilesToRemove{ core *.rwf }
Gaussian-03Command{
setenv MODULEPATH ${MODULEPATH}:/hpc2n/eb/modules/all/Core
ml gaussian
g16 < $infile > $outfile
}

Abisko/HPC2N with ECCE at UMU

You’ll need to have modified ECCE to work with SLURM first. That’s a separate post.

Make sure to run your jobs in /pfs/nobackup/home/X/Username and use /scratch for /scratch

Once you’ve got ECCE modified for SLURM, this is what goes into your CONFIG.abisko file under apps/siteconfig/

NWChem: /lap/nwchem/6.5/bin/nwchem
 Gaussian-03: /hpc2n/eb/software/Core/gaussian/16.A.03-SSE4/g16
 perlPath: /usr/local/bin/
 qmgrPath: /usr/local/bin/
 xappsPath: /usr/local/bin/
Slurm {
 #!/bin/bash
 #SBATCH -A SNIC2017-X-Y
 #SBATCH -c $totalprocs
 #SBATCH -n 1
 #SBATCH --time=$walltime
 #SBATCH --output=job.%J.out
 #SBATCH --error=job.%J.err
 #SBATCH --job-name=$submitFile
 }
NWChemFilesToRemove{ core }
NWChemCommand {
 export PATH=/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin
 hostname
 srun mpirun -n /lap/nwchem/6.5/bin/nwchem $totalprocs $infile > $outfile
 }
Gaussian-03FilesToRemove{ core *.rwf }
Gaussian-03Command{
 module add gaussian
 srun /hpc2n/eb/software/Core/gaussian/16.A.03-SSE4/g16/g16 < $infile > $outfile
 }

(unformatted:

NWChem: /lap/nwchem/6.5/bin/nwchem
Gaussian-03: /hpc2n/eb/software/Core/gaussian/16.A.03-SSE4/g16
perlPath: /usr/local/bin/
qmgrPath: /usr/local/bin/
xappsPath: /usr/local/bin/

Slurm {
#!/bin/bash
#SBATCH -A SNIC2017-X-Y
#SBATCH -c $totalprocs
#SBATCH -n 1
#SBATCH –time=$walltime
#SBATCH –output=job.%J.out
#SBATCH –error=job.%J.err
#SBATCH –job-name=$submitFile
}

NWChemFilesToRemove{ core }

NWChemCommand {
export PATH=/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin
hostname
srun mpirun -n /lap/nwchem/6.5/bin/nwchem $totalprocs $infile > $outfile
}

Gaussian-03FilesToRemove{ core *.rwf }

Gaussian-03Command{
module add gaussian
srun /hpc2n/eb/software/Core/gaussian/16.A.03-SSE4/g16/g16 < $infile > $outfile
}

)

Printing at UMU from Linux

This was done on a debian jessie box with gnome shell

  1. Download the PPD from http://www.openprinting.org/printer/Toshiba/Toshiba-e-Studio_2500c
  2. Go to Print Settings, Unlock and then +Add/Printer
  3. Select Network Printer/Windows Printer via SAMBA
  4. Use smb://kbc-origo.ad.umu.se/kbc-print and make sure to set authentication details. Username should written along the lines of ad.umu.se/abcd0123
  5. Don’t verify, but hit forward.
  6. Under Choose Driver, pick Provide PPD file, and use the file you downloaded in step 1.
  7.  Accept the defaults.
  8.  Due to a new (21/6/2017) and idiotic ‘feature’ of the printing system at UMU (i.e. not linux related) you need to submit the job from a computer account that has the same value as your CAS ID. In plain English: if your linux username is different from your CAS — and it should/will be — you can’t print. To fix this, create /etc/cups/client.conf and put your CAS there, e.g. User abcd1234
  9. You should now be able to print.

Welcome to the Molecular Geochemistry Laboratory

If chemistry is the central science, then geochemistry is the central science as applied to understanding the natural world around us.

Geochemists seek to answer questions relating to the evolution of life on Earth and how metalloenzymes may have evolved, the chemistry of the oceans and how they are affected by global warming, the interplay between flora, fauna and the environment in chemical terms, how pollutants interact with soils and minerals, and how radioactive waste can be securely stored for millennia. We do this by connecting the very big — mountains — with the very small — atoms and molecules, and the very fast — fundamental reactions — with the often very slow — weathering

If you share our passion for understanding and explaining how the world works — join us! To find out about opportunities in our laboratory, contact one of the group leaders: Erik Björn, Jean-François Boily, Michael Holmboe, C. André Ohlin, Andrey Shchukarev, and Staffan Sjöberg.