Thom Group Wiki - User contributions [en]

Background

2020-02-20T16:43:56Z

Ghb29: Note about possible syntax confusion with &

Say you run a qchem program. It may go on for some time. During this time it would be nice to be able to continue using your terminal - perhaps tracking the output of the program.

#Pausing Ctrl-Z will pause your current process.
#Backgrounding bg will cause your currently paused process will be restarted in the background.
#The & The & symbol at the end of an input will automatically run the program in the background. E.g. qchem ''input'' ''output'' &
#* <code>&</code> ends a command, so you can't use it next to <code>;</code>, which also ends a command. So <code>for i in a b; do echo $i &; done</code> is a syntax error; the semicolon after the <code>&</code> must be deleted.
#jobs This command shows all the processes running in the background. The id's are given for use with...
#Foregrounding fg will cause one currently backgrounded process to be brought back the foreground - perhaps to be Ctrl-C killed.
#top If you lose track of your processes running in the background, perhaps because your connection through ssh was reset, you can see all processes running on the computer with top. From here you can kill processes with 'k' + the PID listed. For more information see the top link under the introduction page.

QChem

2020-02-20T15:53:18Z

Ghb29: Document producing INTDUMP files

Q-Chem is a commercial quantum chemistry package available for use in our group.

= Fragment Guesses with multiple bases =
To uses basis set projection and fragment guesses you have to run the smaller basis set calculation with fragments first, and then read this into a second calculation which does the projection
<code>
$molecule
0 1
--
0 1
H 0.000000 -0.115747 1.133769
H 0.000000 1.109931 -0.113383
O 0.000000 0.005817 -0.020386
--
0 1
He 10000 0 0
$end
$rem
JOBTYPE sp
EXCHANGE b3lyp
BASIS cc-pVDZ
scf_guess fragmo
CORRELATION none
SYMMETRY false
SYM_IGNORE true
$end
@@@
$molecule
read
$end
$rem
scf_guess read
JOBTYPE sp
EXCHANGE b3lyp
BASIS cc-pVTZ
BASIS2 cc-pVDZ
CORRELATION none
MAX_SCF_CYCLES 600
SYMMETRY false
SYM_IGNORE true
basisprojtype ovprojection
$end
</code>

==INTDUMP / FCIDUMP ==

To create files in the FCIDUMP format (used e.g. by Hande) create a QChem input file:

<pre>
$molecule
0 1
H 0 0 0
H 1 0 0
$end

$rem
correlation idump
exchange hf
basis sto-3G
use_abelian_subgroup true
scf_guess_print 9999
$end
</pre>

and use the version of QChem currently (2020-02-20) available from:
<pre>
[you@liminal] $ export QC=public_o
[you@liminal] $ source ~ajwt3/code/qchem/qcsetup.bash
[you@liminal] $ qchem your-input-file.in
</pre>

This should produce a file called <code>INTDUMP</code>
<pre>
&FCI NORB= 2,NELEC= 2,MS2= 0
ORBSYM=1,6,
ISYM=1 UHF=.FALSE.
&END
0.62640249948715 1 1 1 1
0.19679058349422 1 2 1 2
0.6217067630807 2 2 1 1
0.19679058349422 2 1 1 2
0.19679058349422 2 1 2 1
0.65307074688898 2 2 2 2
-1.1108441795661 1 1 0 0
-0.58912100326925 2 2 0 0
-0.39980670964291 1 0 0 0
0.37823811728909 2 0 0 0
0.52917721026434 0 0 0 0
</pre>

Computer and Storage List

2020-02-20T09:34:06Z

Ghb29: Add cerberus info

{|
!name
!user
!cores
!processor
!RAM
!OS
|-
|carpathia
|Alex
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 14.04.3
|-
|liminal
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|hypatia
|Ruth
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 16.04
|-
|serenity
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 16.04
|-
|sandstone
|Charlie
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 14.04.3
|-
|gritstone
|Verena
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 16.04.4
|-
|moonraker
|Alex G
|4
|Intel(R) Xeon(R) E3-1270 v5 CPU @ 3.66GHz
|64GB
|Ubuntu 16.04
|-
|obsidian
|Hugh
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04
|-
|hylas
|Fabio
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 16.04
|-
|cerberus
|Alex
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|David
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|chesterian
|Bang
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 16.04.3
|-
|nemesis
|Rhiannon
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 16.04.3
|-
|cerebro
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9)

HANDE

2020-02-20T00:51:15Z

Ghb29: /* Github releases */ typo

Information about HANDE releases and running tests.

== Github releases ==

Releases are pushed to [https://www.github.com/hande-qmc/hande Github] approx. every 6 months.
* Create a new file in the release_notes folder in the documentation, e.g. v1.4.rst, to describe what features have been added, changed, removed and what bugs have been fixed since the last release. Do this on a branch, ideally do a small pull request, merge to (private) master.
* Ideally, recreate the benchmarks for the testsuite. To save time: do one run in optimised/non-debug mode, then do the debug tests. Or do all in debug mode. Need to be able to run the FCI tests. Again, doing this on a branch is probably cleanest.
* Merge the public branch into the private master to keep a single history.
* Update file `tools/configurator.py` to say the next version (e.g. 1.4 instead of 1.3).
* Tag this version as e.g. v1.4 (`git tag -a v1.4` - https://git-scm.com/book/en/v2/Git-Basics-Tagging).
* Merge that updated private master into public master.
* Update the hande-www repository to update the HANDE website. Update github documentation if required.

== Buildbot ==

The tests are run nightly by [http://www.cmth.ph.ic.ac.uk/buildbot/hande/grid buildbot]. To update the configuration, edit
<pre>
hande_master@zeeman.cmth.ph.ic.ac.uk:hande/master.cfg
</pre>

Remember to restart the buildbot afterwards:
<pre>
buildbot restart
</pre>

Other relevant accounts are the account the slaves connect to by ssh: hande@zeeman, and the account the CUC3 buildslave runs on: jss43@hypatia. This latter may need the buildslave restarted each time hypatia is rebooted:
<pre>
buildslave start
</pre>

== Website ==

The [http://www.hande.org.uk website] uses rst and Nikola. The source on [https://www.github.com/hande-qmc/hande-www github]. To update, edit the rst files (currently there is only a main page: to create others simply add more files to the pages/ folder), commit the changes and run
<pre>
nikola github_deploy
</pre>

== Running the test suite on cerebro ==

Make use of other people having done the work for you:
<pre>
cd
ln -s ~ajwt3/privatemodules
</pre>

Then load these modules (to test with the tough gfortran compiler and mpi):
<pre>
module load use.own

module unload gcc
module load gcc/6.4.0

module unload mpi
module load mpi/openmpi/gnu6/3.0.0
module load anaconda/python2/4.4.0

module unload lua
module load lua/5.3.4/gcc-4.8.3
module load mkl/64/2017/0/4

module unload trlan
module load trlan/201009/gcc-6.4.0

module unload hdf5
module load hdf5/1.8.20/gcc-6.4.0
</pre>

This config works for AJWT on cerebro as of 5/2/19 for intel
<pre>
module unload gcc
module load gcc/4.8.3
module unload icc
module load icc/64/2019/1

module load use.own
module unload mpi
module load mpi/hack-openmpi/intel17/3.1.2
module load anaconda/python2/4.4.0
module unload lua mkl hdf5 trlan
module load lua/5.3.4 mkl/64/2017/0/4 hdf5/1.8.20/ifort2017_5 trlan/201009/ifort2017_5
</pre>

Compile HANDE with these files modified ("git diff") using config/gfortran.mkl.mpi.pop64:
<pre>
diff --git a/config/gfortran.mkl.mpi.pop64 b/config/gfortran.mkl.mpi.pop64
index 065d1a3..cf79d05 100644
--- a/config/gfortran.mkl.mpi.pop64
+++ b/config/gfortran.mkl.mpi.pop64
@@ -1,5 +1,5 @@
[DEFAULT]
-include_f = -I $${HDF5_ROOT-/usr}/include -std=f2008ts
+include_f = -I $${HDF5_ROOT}/include -std=f2008ts
cppflags_opt = -DHAVE_SSE2 -DPARALLEL -DDET_SIZE=64 -DPOP_SIZE=64 -DDSFMT_MEXP=19937

[main]
@@ -7,7 +7,8 @@ fc = mpif90
cc = mpicc
cxx = mpiCC
ld = mpif90
-libs = -ltrlan_mpi -lmkl_scalapack_lp64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -Wl,--end-group -lpthread -lstdc++ -lhdf5_fortran -luui
+libs = -ltrlan_mpi ${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a ${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a ${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_gf_lp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -lgomp -lpthread -lm -ldl -luuid -llua -lstdc++ -lhdf5_fortran
f90_module_flag = -J

[opt]
diff --git a/test_suite/userconfig b/test_suite/userconfig
index 80452b1..9c39799 100644
--- a/test_suite/userconfig
+++ b/test_suite/userconfig
@@ -8,6 +8,7 @@ ignore_fields = time
skip_program = grep
skip_args = -i 'disabled at compile-time\|Fatal: not compiled with HDF5 support\|Running with .* threads\|Tried to pass logging options to a non-debug build'
skip_cmd_template = tc.skip tc.args tc.test tc.error
+launch_parallel = srun -N1 -p TEST -n tc.nprocs

[user]
diff = vimdiff
</pre>

and then run the test suite with
<pre>
../../testcode/bin/testcode.py -cpop64_mpi --total-processors=120 --processors=1
</pre>
To run just one test, e.g. nh3.ccsdt.ppN.in,
<pre>
srun -n4 -N1 ~/code/hande/bin/hande.x nh3.ccsdt.ppN.in
</pre>

User:Ghb29

2019-11-19T15:21:50Z

Ghb29:

George Bateman, Part III student AY2019-2020.

User:Ghb29

2019-11-19T15:21:44Z

Ghb29: Created page with "George Bateman, Pat III student AY2019-2020."

George Bateman, Pat III student AY2019-2020.

Tyche

2019-11-19T15:21:18Z

Ghb29: Document quartus license issue

'''Tyche''' is a piece of software currently hosted [https://gitlab.developers.cam.ac.uk/ch/thom/tyche on the Cambridge GitLab] which is able to carry out quantum Monte Carlo calculations. It supports Diffusion Monte Carlo (DMC) and Variational Monte Carlo (VMC). It can be compiled for CPU usage alone (C) or for use on a FPGA (written in MaxJ and C).

==Installation (FPGA)==

CentOS 6 or 7 is required.

===Altera Quartus===
Intel (formerly Altera) Quartus is used to compile to a hardware layout on the chip. If using the currently recommended 13.1 version on modern Linux systems then it may fail to recognise your MAC address; this means <code>lmutil lmhostid</code> will give a blank/zero id and code will not compile.

It has a network card-linked license which assumes that your network interfaces are named with the old <code>eth0</code> convention. To achieve this <code>sudoedit /etc/default/grub</code>, append <code> net.ifnames=0 biosdevname=0</code> to <code>GRUB_CMDLINE_LINUX</code>, run <code>sudo grub2-mkconfig -o /boot/grub2/grub.cfg</code>, and reboot. (Source: https://www.schrodinger.com/kb/1649)