ChemWiki - User contributions [en]

Mod:Hunt Research Group/calendar

2018-03-19T09:49:17Z

Ic1517:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Done)
| Ken (Done)
| Becky (Not Done)
|-
| Sophie (Done)
| Lennart (Not Done)
| Oxana (Done)
|-
| Sanha (Done)
| Nerissa (Not Done)
|Inyoung (Not Done)
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away

Lennart in South Africa

Oxana away
|19th
Sophie Away

Lennart in South Africa

Oxana away
|20th
Sophie Away

Lennart in South Africa

Oxana away
|21st
Sophie Away

Lennart in South Africa

Oxana away
|22nd
Sophie Away

Lennart in South Africa

Oxana away

Ken Away
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open

Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|3rd
Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|4th
Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|5th
Tricia Away

Lennart in South Africa

Ken Away

Nerissa Away
| style="background: grey;" |6th
| style="background: grey;" |7th
|-
|8th Jan
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

Oxana Exam
|9th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week
|10th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week
|11th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

'''Tricia Belfast'''
|12th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

'''Tricia Belfast'''
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|15th
|16th
|17th
'''Tricia York'''
|18th
|19th
| style="background: grey;" |20th
| style="background: grey;" |21st
|-
|22nd
|23rd
'''Tricia AWE meeting'''
|24th
|25th
|26th
'''Tricia Beijing'''
| style="background: grey;" |27th
| style="background: grey;" |28th
|-
|29th
'''Tricia Beijing'''
|30th
'''Tricia Beijing'''
|31st
'''Tricia Beijing'''
| style="background: yellow;" |1st Feb
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
'''Tricia Manchester'''
|8th
|9th
'''Academic visitor'''
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
'''Tricia on course'''
|13th
|14th
|15th
|16th
Sophie at TYC student day
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
Sophie DL_SOFTWARE

training course
|20th
Sophie DL_SOFTWARE

training course
|21st
Sophie DL_SOFTWARE

training course
|22nd
'''Tricia York'''

Sophie DL_SOFTWARE

training course
|23rd
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
|27th
|28th
Oxana away
| style="background: yellow;" |1st Mar
Oxana away
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
|8th
'''Tricia on course'''
|9th
'''Tricia on course'''
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
|13th
|14th
Oxana away
|15th
Oxana away
|16th
Oxana away
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
|20th
'''Tricia CECAM conf.'''
|21st
'''Tricia CECAM conf.'''
|22nd
'''Tricia CECAM conf.'''
|23rd
'''Tricia CECAM conf.'''
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
Oxana away

Inyoung away
|27th
Oxana away

Inyoung away
|28th
Oxana away

Inyoung away
|29th College Closed
|30th College Closed
Good Friday
| style="background: grey;" |31st
| style="background: yellow;" |1st Apr
Easter Sunday
|-
|}

Mod:Hunt Research Group/calendar

2018-02-19T11:24:35Z

Ic1517:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Done)
| Ken (Done)
| Becky (Not Done)
|-
| Sophie (Done)
| Lennart (Not Done)
| Oxana (Done)
|-
| Sanha (Done)
| Nerissa (Not Done)
|Inyoung (Not Done)
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away

Lennart in South Africa

Oxana away
|19th
Sophie Away

Lennart in South Africa

Oxana away
|20th
Sophie Away

Lennart in South Africa

Oxana away
|21st
Sophie Away

Lennart in South Africa

Oxana away
|22nd
Sophie Away

Lennart in South Africa

Oxana away

Ken Away
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open

Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|3rd
Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|4th
Tricia Away

Lennart in South Africa

Oxana away

Ken Away

Nerissa Away
|5th
Tricia Away

Lennart in South Africa

Ken Away

Nerissa Away
| style="background: grey;" |6th
| style="background: grey;" |7th
|-
|8th Jan
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

Oxana Exam
|9th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week
|10th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week
|11th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

'''Tricia Belfast'''
|12th
Nerissa Exam Week

Inyoung Exam Week

Sanha Exam Week

'''Tricia Belfast'''
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|15th
|16th
|17th
'''Tricia York'''
|18th
|19th
| style="background: grey;" |20th
| style="background: grey;" |21st
|-
|22nd
|23rd
'''Tricia AWE meeting'''
|24th
|25th
|26th
'''Tricia Beijing'''
| style="background: grey;" |27th
| style="background: grey;" |28th
|-
|29th
'''Tricia Beijing'''
|30th
'''Tricia Beijing'''
|31st
'''Tricia Beijing'''
| style="background: yellow;" |1st Feb
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
'''Tricia Manchester'''
|8th
|9th
'''Academic visitor'''
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
'''Tricia on course'''
|13th
|14th
|15th
|16th
Sophie at TYC student day
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
Sophie DL_SOFTWARE

training course
|20th
Sophie DL_SOFTWARE

training course
|21st
Sophie DL_SOFTWARE

training course
|22nd
'''Tricia York'''

Sophie DL_SOFTWARE

training course
|23rd
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
|27th
|28th
Oxana away
| style="background: yellow;" |1st Mar
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
|8th
'''Tricia on course'''
|9th
'''Tricia on course'''
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
|13th
|14th
|15th
|16th
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
|20th
'''Tricia CECAM conf.'''
|21st
'''Tricia CECAM conf.'''
|22nd
'''Tricia CECAM conf.'''
|23rd
'''Tricia CECAM conf.'''
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
Oxana away
|27th
Oxana away
|28th
Oxana away
|29th College Closed
|30th College Closed
Good Friday
| style="background: grey;" |31st
| style="background: yellow;" |1st Apr
Easter Sunday
|-
|}

Mod:Hunt Research Group/hpc

2018-01-19T17:32:39Z

Ic1517: /* Recommended specifications */

=Running jobs on the Imperial HPC=
Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== Queues to run on ==
:'''pqph''' (various, see below) this is the hunt group queue, runs on the servers listed below
::each user has can have a '''maximum of 12 running jobs'''
::to help balance usage please have a '''maximum of 20 jobs running or qued'''
:'''pqchem''' (42 nodes) this is the chemistry department queue,
:'''chemlab1''' (2 chassis) this is for the computational chemistry lab but can be used out of term time
:which can be accessed from https://scanweb.cc.ic.ac.uk/

== Using qstat ==
:qstat to get your jobs that are running
:qstat -q to get a list of all queues
:qdel and ID number to remove a job from the queue
:a short script to list all the queues in one command
::type qstatme and it will list the info for the three queues pqph, chemlab1 and pqchem
<pre>[phunt@login-3-internal]/home/phunt/bin $ cat qstatme
#!/bin/bash
#
qstat -q | grep 'pqph '
qstat -q | grep 'chemlab1 '
qstat -q | grep 'pqchem '
</pre>

== Submit script uses PBS queing==
*everyone should START by using this script, and not the automated submission script (see later)
*have a copy of this script in the directory you are running the job from
*here is an example called rng16_66
<pre>[phunt@login-3-internal]/work/phunt/ $ cat rng16_66
#!/bin/sh

# submit jobs to the que with this script using the following command:
# qsub -N jobname -v in=name rng16_66
# rng16_66 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in}

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=16:mem=64000MB
#PBS -j oe
#PBS -q pqph

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directoiry from which the job was sumbited.
test -r $PBS_O_WORKDIR/${in}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in}.chk"
cp $PBS_O_WORKDIR/${in}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in}.chk"
fi
#
# run gaussian
#
pbsexec g09 $PBS_O_WORKDIR/${in}.com
#
# job has ended copy back the checkpoint file
# check to see if there are other external files like .wfn or .mos and copy these as well
#
cp $TMPDIR/${in}.chk /$PBS_O_WORKDIR/.
test -r $TMPDIR/${in}.wfn
if [ $? -eq 0 ]
then
cp $TMPDIR/${in}.wfn /$PBS_O_WORKDIR/${in}.wfn
fi
test -r $TMPDIR/fort.7
if [ $? -eq 0 ]
then
cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in}.mos
fi
# exit
</pre>

Without "#!/bin/sh" in the beginning of the job script, the job will always go to the queue "short" instead of the queue asked for.

==ONLY once you have used the queuing script for some time==
*use the gf script created by Giacommo made which makes it easier to submit jobs to the hpc.
*The link below contains the script and instructions for using it.
::https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/pimpQSUB

== Comments on the PBS ==
\#PBS -l walltime=119:59:00
*the -l walltime is the maximum time the job will run in seconds it will be killed at the walltime
*pqph has a very long walltime, other queues have a shorter walltime, adjust as necessary

\#PBS -q pqph
*the -q option tells it which queue to run on adjust as necessary

\#PBS -lselect=1:ncpus=16:mem=64000MB
*this is a very important line!
*lselect=1 means run on one node
*ncpus=the number of cpus
*mem=the maximum amount of memory
*these are specific to each node,
**it is important that you manage your usage properly to not waste resources and to allow efficient usage when there is a backlog of jobs
**decide on the size of your job, do you need many processors and lots of memory? if not run on a smaller node!
**use [https://www.hpc.imperial.ac.uk/selfservice/cx1/pqadmin/pqph/nodes nodes] to select which node you want to run on
**set the ncpus and mem appropriately (see below)
**note that you cannot use as much memory as is indicated in the Node status table, always request slightly less
*sometimes the job does not go in properly if you use GB so always use MB in your specification
**1GB=1000MB

\#PBS -j oe
•merge the standard output and error files

==Servers==
:pqph has
:::12 nodes 94GB 12 proc
:::8 nodes 62GB 16 proc
:::4 nodes 125GB 20 proc (1 node is out of action)
:::4 nodes 151GB 24 proc
:::4 nodes 125GB 40 proc

:pqchem has
:::2 nodes with 16cpus 66 GBytes memory 200 GByte disk
:::5 nodes with 12cpus 99 GBytes memory 800 GByte disk
:::4 nodes with 12cpus 50 GBytes memory 800 GByte disk
:::10 nodes with 20cpus 132 GBytes memory 1800 GByte disk

== Recommended specifications ==

*Gaussian is greedy and will exceed the allocated memory
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

in the following
: the first line gives the processor and memory
: the second line the amount to allocate in the PBS script
: the third and fourth lines the amount to allocated in the gaussian com file

:'''For very small''' jobs use half a 12 proc 94 GB node
::\#PBS -lselect=1:ncpus=6:mem=46000MB
::%nprocs=6
::%mem=45000MB

:'''Small jobs''' 12 nodes: 12 cpu 94 GB (100 GB decimal)
::\#PBS -lselect=1:ncpus=12:mem=92000MB
::%nprocs=12
::%mem=90000MB

:'''Medium level jobs''' 8 nodes: 16 cpu 62 GB (65 GB decimal)
::\#PBS -lselect=1:ncpus=16:mem=60000MB
::%nprocs=16
::%mem=58000MB

:'''Big processor jobs''' 4 nodes: 40 cpu 125 GB (132 GB decimal)
::\#PBS -lselect=1:ncpus=40:mem=121000MB
::%nprocs=40
::%mem=118000MB

:'''Large memory jobs''' 8 nodes: 20 cpu 125 GB (132 GB decimal)
::\#PBS -lselect=1:ncpus=20:mem=123000MB
::%nprocs=20
::%mem=120000MB

:'''Largest jobs''' 4 nodes: 24 cpu 251 GB (264 GB decimal)
::\#PBS -lselect=1:ncpus=24:mem=248000MB
::%nprocs=24
::%mem=245000MB

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal)

==more details for if you seem to be having memory or disk issues==
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

== checkpoint and other files ==
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/calendar

2017-11-20T21:09:24Z

Ic1517: /* Calendar */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia
| Ken (Not Done)
| Becky (Done)
|-
| Sophie
|
|
|-
|
|
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|16th Oct
|17th
|18th
|19th
|20th
Ken Away
| style="background: grey;" |21st
| style="background: grey;" |22nd
|-
|23rd Tricia in Spain
|24th Tricia in Spain
|25th Tricia in Spain
|26th Tricia in Spain
|27th Tricia in Spain Oxana away
| style="background: grey;" |28th
| style="background: grey;" |29th
|-
|30th
|31st
| style="background: yellow;" |1st Nov
|2nd
|3rd
| style="background: grey;" |4th
| style="background: grey;" |5th
|-
|6th
|7th
|8th
|9th
|10th Tricia at Nottingham
| style="background: grey;" |11th
| style="background: grey;" |12th
|-
|13th
|14th
|15th
|16th
|17th
| style="background: grey;" |18th
| style="background: grey;" |19th
|-
|20th
Sophie Away
|21st
|22nd
|23rd
Inyoung in Iceland
|24th
Inyoung in Iceland
| style="background: grey;" |25th
| style="background: grey;" |26th
|-
|27th
|28th
|29th
|30th
| style="background: yellow;" |1st Dec
| style="background: grey;" |2nd
| style="background: grey;" |3rd
|-
|4th Tricia in Germany
|5th Tricia in Germany
|6th Tricia in Germany
|7th Tricia in Germany
|8th Tricia in Germany
Ken Away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away
|19th
Sophie Away
|20th
Sophie Away
|21st
Sophie Away
|22nd
Sophie Away
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open
|3rd
|4th
|5th
| style="background: grey;" |6th
| style="background: grey;" |7th
|}