=== Making movies in VMD ===

'''General stuff:'''
* Animated gifs can be dropped into Power Point or into a browser to play. I normally used this format.
* mp4 movies are also OK
* Unusual (and very beautiful) representations can be created in VMD using renderers other than Snapshot, but they take longer to produce, so I don't mention them here.
* In all cases, load the relevant trajectories and format how it looks.
* In VMD Main→Display→Render Mode, chose GLSL to enable transparent materials.
* Save the visualization state as a *vmd file, in case you want to make modifications in the future.
* There are specialized tutorials to learn how to use the visualization capabilities of VMD. Search for them... Here I only summarize a few topics for which guidelines appear to be harder to find.

'''Drawing an arrow at the pulled end (for pulling simulations)'''

In pulling simulations, it is sometimes useful to draw an arrow at the pulled end for visualization purposes. Steps to do this in VMD:

# Modify script script_drawArrow.tcl to your needs, to specify the atom where the arrow starts and direction of arrow.
# Run script (by typing at the VMD TkConsole "source script_drawArrow.tcl "; the "" are not typed in...)
# Move the bar in VMD main from the beginning to the end of the trajectory, so the script executes for each frame

''' Update the secondary structure at every frame'''

Some representations (e.g. NewCartoon) depend on the secondary structure of the amino acids, but by default VMD does not update it every frame to keep things light. If you need it updated at every frame:

# Save the script [https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/sscache.tcl sscache.tcl ] somewhere in your machine, and then source it within VMD (by typing at the VMD Tkconsole "source sscache.tcl")
# Source the script named [https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/stride.tcl stride.tcl] (in the same way as in 1)
# Type at the TkConsole "start_sscache"
# Move the bar in VMD main from the beginning to the end of the trajectory, so the SS is cached. You should be able to see now that it is updated at every frame.

To turn off the trace, use the command stop_sscache, which also takes the molecule number. There must be one stop_sscache for each start_sscache. The command clear_sscache resets the saved secondary structure data for all the molecules and all the frames. More info in https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node256.html

'''Making movies (A)'''

This option is OK for trajectories that are not too jumpy to begin with.

In VMD Main → Extensions → Movie Maker:
# renderer snapshot
# movie settings: trajectory ; leave option to delete all files on
# format: Animated GIF (image magick)
# Select an empty working directory
# Click on "Make Movie", and wait until it completes

'''Making movies (B)'''

This option is better if your trajectory is jumpy.

Step 1: In VMD Main → Extensions → Move Maker:
# renderer snapshot
# movie settings: trajectory ; deselect option to delete all files
# format: jpeg (image magick)
# Select an empty working directory
# Click on "Make Movie", and wait until it completes

Step 2: In a Linux machine, in the directory with the jpeg images, run command
convert -delay 30 myImageName.*.jpg myMovie-delay-30.gif

Try several delay values (5 to 50 is a good range) to find something that works. Remember to rename the movies according to the delay so at the end you can chose the best one.

2022-03-13T08:47:43Z

Brendel: +OpenMPI

A-Cluster

2022-03-09T10:21:03Z

Brendel: storage

Linux cluster with currently 13 compute nodes (CPUs: 416 cores, GPUs: 8x RTX 2080 + 18x RTX 3090) and 2×251TiB disk storage, purchased by Ana Vila Verde and Christopher Stein

= Login =

External Hostname is <code>a-cluster.physik.uni-due.de</code> (134.91.59.16), internal hostname is <code>stor2</code>.

= Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =

* There are two queues (''partitions'' in Slurm terminology) named:
** ''CPUs'', the default
** ''GPUs'', to be selected via <code>-p GPUs</code> for jobs which involve a GPU
* <code>[https://slurm.schedmd.com/sinfo.html sinfo]</code> displays the cluster's total load.
* <code>[https://slurm.schedmd.com/squeue.html squeue]</code> shows running jobs. You can modify its output via the option <code>-o</code>. To make that permanent put something like <code>alias squeue='squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C %o"'</code> into your <code>.bashrc</code>.
* In the most simple cases, jobs are submitted via <code>[https://slurm.schedmd.com/sbatch.html sbatch] -n</code> ''n'' ''script-name''. The number ''n'' of CPUs is available within the script as <code>$SLURM_NTASKS</code>. It's not necessary to pass it on to <code>mpirun</code>, since the latter evaluates it on its own, anyway.
* To allocate GPUs as well, add <code>-G </code>''n'' or <code>--gpus=</code>''n'' with ''n'' ∈ {1,2}. You can specify the type as well by prepending <code>rtx2080:</code> or <code>rtx3090:</code> to ''n''.
* Don't use background jobs (<code>&</code>), unless you <code>wait</code> for them before the end of the script.
* <code>[https://slurm.schedmd.com/srun.html srun]</code> is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its <code>-n</code> doesn't only reserve ''n'' cores but starts ''n'' jobs. (Those shouldn't contain <code>mpirun</code>, otherwise you'd end up with ''n''² busy cores.)
* For an interactive shell with ''n'' reserved cores on a compute node: <code>srun --pty -c</code>''n''<code> bash</code>
* The assignment of cores can be non-trivial (cf. also [[Slurm/Task-Affinity|task affinity]]), some rules:
** gromacs: '''Don't''' use its <code>-pin</code> options.

= Scientific Software =

... installed (on the ''compute nodes'')

== AMBER ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

* <code>/usr/local/amber18</code>
* <code>/usr/local/amber20</code> (provides <code>parmed</code> as well)

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>amber.sh</code>

== GROMACS ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

Versions (not all tested):

* <code>/usr/local/gromacs-2018.3</code>
* <code>/usr/local/gromacs-2020.4</code>
* <code>/usr/local/gromacs-3.3.4</code>
* <code>/usr/local/gromacs-4.6.4</code>
* <code>/usr/local/gromacs-5.0.1</code>
* <code>/usr/local/gromacs-5.1.1</code>

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>bin/GMXRC.bash</code>

Ana provided an [https://wiki.uni-due.de/vilaverde/index.php/File:Gromacs_cpu.sh example script] to be submitted via <code>sbatch</code>.

== OpenMolcas ==

(compiled with Intel compiler and MKL)

Minimal example script to be <code>sbatch</code>ed:

#!/bin/bash

export MOLCAS=/usr/local/openmolcas
export MOLCAS_WORKDIR=/tmp/$USER-$SLURM_JOB_NAME-$SLURM_JOB_ID
mkdir $MOLCAS_WORKDIR
export PATH=$PATH:$MOLCAS
export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/mkl/latest/lib/intel64
export OMP_NUM_THREADS=${SLURM_NTASKS:-1}

pymolcas the_input.inp

rm -rf $MOLCAS_WORKDIR

If you want/need to use the module system instead of setting <code>LD_LIBRARY_PATH</code> manually:

shopt -s expand_aliases
source /etc/profile.d/modules.sh

module use /opt/intel/oneapi/modulefiles
module -s load compiler/latest
module -s load mkl/latest

= Intel Compiler & Co. =

* is located in <code>/opt/intel/oneapi</code>
* must be made available via <code>module use /opt/intel/oneapi/modulefiles</code> (unless you include <code>/opt/intel/oneapi/modulefiles</code> in your <code>MODULEPATH</code>), then <code>module avail</code> lists the available modules.

= Backups =

A backup of the users' home directories is taken nightly. To access the
backups, first log in to the cluster. Then:
* Users in <code>/home/stor.vd1</code>: Last night's backup is in <code>/export/vd1/$USER</code>.
* Users in <code>/home/stor1.lv0</code>: You actually have seven backups corresponding to the last 7 days in <code>/exports/lv0/snapshots/days.''D''/stor1/home/stor1.lv0/$USER</code> with ''D'' $\in\{0,\dots,6\}$.

A-Cluster

2022-03-09T10:15:40Z

Brendel: /* Backups */ vd1

Linux cluster with currently 13 compute nodes (CPUs: 416 cores, GPUs: 8x RTX 2080 + 18x RTX 3090), purchased by Ana Vila Verde and Christopher Stein

= Login =

External Hostname is <code>a-cluster.physik.uni-due.de</code> (134.91.59.16), internal hostname is <code>stor2</code>.

= Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =

* There are two queues (''partitions'' in Slurm terminology) named:
** ''CPUs'', the default
** ''GPUs'', to be selected via <code>-p GPUs</code> for jobs which involve a GPU
* <code>[https://slurm.schedmd.com/sinfo.html sinfo]</code> displays the cluster's total load.
* <code>[https://slurm.schedmd.com/squeue.html squeue]</code> shows running jobs. You can modify its output via the option <code>-o</code>. To make that permanent put something like <code>alias squeue='squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C %o"'</code> into your <code>.bashrc</code>.
* In the most simple cases, jobs are submitted via <code>[https://slurm.schedmd.com/sbatch.html sbatch] -n</code> ''n'' ''script-name''. The number ''n'' of CPUs is available within the script as <code>$SLURM_NTASKS</code>. It's not necessary to pass it on to <code>mpirun</code>, since the latter evaluates it on its own, anyway.
* To allocate GPUs as well, add <code>-G </code>''n'' or <code>--gpus=</code>''n'' with ''n'' ∈ {1,2}. You can specify the type as well by prepending <code>rtx2080:</code> or <code>rtx3090:</code> to ''n''.
* Don't use background jobs (<code>&</code>), unless you <code>wait</code> for them before the end of the script.
* <code>[https://slurm.schedmd.com/srun.html srun]</code> is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its <code>-n</code> doesn't only reserve ''n'' cores but starts ''n'' jobs. (Those shouldn't contain <code>mpirun</code>, otherwise you'd end up with ''n''² busy cores.)
* For an interactive shell with ''n'' reserved cores on a compute node: <code>srun --pty -c</code>''n''<code> bash</code>
* The assignment of cores can be non-trivial (cf. also [[Slurm/Task-Affinity|task affinity]]), some rules:
** gromacs: '''Don't''' use its <code>-pin</code> options.

= Scientific Software =

... installed (on the ''compute nodes'')

== AMBER ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

* <code>/usr/local/amber18</code>
* <code>/usr/local/amber20</code> (provides <code>parmed</code> as well)

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>amber.sh</code>

== GROMACS ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

Versions (not all tested):

* <code>/usr/local/gromacs-2018.3</code>
* <code>/usr/local/gromacs-2020.4</code>
* <code>/usr/local/gromacs-3.3.4</code>
* <code>/usr/local/gromacs-4.6.4</code>
* <code>/usr/local/gromacs-5.0.1</code>
* <code>/usr/local/gromacs-5.1.1</code>

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>bin/GMXRC.bash</code>

Ana provided an [https://wiki.uni-due.de/vilaverde/index.php/File:Gromacs_cpu.sh example script] to be submitted via <code>sbatch</code>.

== OpenMolcas ==

(compiled with Intel compiler and MKL)

Minimal example script to be <code>sbatch</code>ed:

#!/bin/bash

export MOLCAS=/usr/local/openmolcas
export MOLCAS_WORKDIR=/tmp/$USER-$SLURM_JOB_NAME-$SLURM_JOB_ID
mkdir $MOLCAS_WORKDIR
export PATH=$PATH:$MOLCAS
export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/mkl/latest/lib/intel64
export OMP_NUM_THREADS=${SLURM_NTASKS:-1}

pymolcas the_input.inp

rm -rf $MOLCAS_WORKDIR

If you want/need to use the module system instead of setting <code>LD_LIBRARY_PATH</code> manually:

shopt -s expand_aliases
source /etc/profile.d/modules.sh

module use /opt/intel/oneapi/modulefiles
module -s load compiler/latest
module -s load mkl/latest

= Intel Compiler & Co. =

* is located in <code>/opt/intel/oneapi</code>
* must be made available via <code>module use /opt/intel/oneapi/modulefiles</code> (unless you include <code>/opt/intel/oneapi/modulefiles</code> in your <code>MODULEPATH</code>), then <code>module avail</code> lists the available modules.

= Backups =

A backup of the users' home directories is taken nightly. To access the
backups, first log in to the cluster. Then:
* Users in <code>/home/stor.vd1</code>: Last night's backup is in <code>/export/vd1/$USER</code>.
* Users in <code>/home/stor1.lv0</code>: You actually have seven backups corresponding to the last 7 days in <code>/exports/lv0/snapshots/days.''D''/stor1/home/stor1.lv0/$USER</code> with ''D'' $\in\{0,\dots,6\}$.

A-Cluster

2022-03-09T09:01:02Z

Brendel: Backups

Linux cluster with currently 13 compute nodes (CPUs: 416 cores, GPUs: 8x RTX 2080 + 18x RTX 3090), purchased by Ana Vila Verde and Christopher Stein

= Login =

External Hostname is <code>a-cluster.physik.uni-due.de</code> (134.91.59.16), internal hostname is <code>stor2</code>.

= Queueing system: [https://slurm.schedmd.com/documentation.html Slurm] =

* There are two queues (''partitions'' in Slurm terminology) named:
** ''CPUs'', the default
** ''GPUs'', to be selected via <code>-p GPUs</code> for jobs which involve a GPU
* <code>[https://slurm.schedmd.com/sinfo.html sinfo]</code> displays the cluster's total load.
* <code>[https://slurm.schedmd.com/squeue.html squeue]</code> shows running jobs. You can modify its output via the option <code>-o</code>. To make that permanent put something like <code>alias squeue='squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C %o"'</code> into your <code>.bashrc</code>.
* In the most simple cases, jobs are submitted via <code>[https://slurm.schedmd.com/sbatch.html sbatch] -n</code> ''n'' ''script-name''. The number ''n'' of CPUs is available within the script as <code>$SLURM_NTASKS</code>. It's not necessary to pass it on to <code>mpirun</code>, since the latter evaluates it on its own, anyway.
* To allocate GPUs as well, add <code>-G </code>''n'' or <code>--gpus=</code>''n'' with ''n'' ∈ {1,2}. You can specify the type as well by prepending <code>rtx2080:</code> or <code>rtx3090:</code> to ''n''.
* Don't use background jobs (<code>&</code>), unless you <code>wait</code> for them before the end of the script.
* <code>[https://slurm.schedmd.com/srun.html srun]</code> is intended for interactive jobs (stdin+stdout+stderr stay attached to the terminal) and its <code>-n</code> doesn't only reserve ''n'' cores but starts ''n'' jobs. (Those shouldn't contain <code>mpirun</code>, otherwise you'd end up with ''n''² busy cores.)
* For an interactive shell with ''n'' reserved cores on a compute node: <code>srun --pty -c</code>''n''<code> bash</code>
* The assignment of cores can be non-trivial (cf. also [[Slurm/Task-Affinity|task affinity]]), some rules:
** gromacs: '''Don't''' use its <code>-pin</code> options.

= Scientific Software =

... installed (on the ''compute nodes'')

== AMBER ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

* <code>/usr/local/amber18</code>
* <code>/usr/local/amber20</code> (provides <code>parmed</code> as well)

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>amber.sh</code>

== GROMACS ==

The [https://modules.readthedocs.io/en/latest module system] is not involved. Instead, scripts provided by the software set the environment.

Versions (not all tested):

* <code>/usr/local/gromacs-2018.3</code>
* <code>/usr/local/gromacs-2020.4</code>
* <code>/usr/local/gromacs-3.3.4</code>
* <code>/usr/local/gromacs-4.6.4</code>
* <code>/usr/local/gromacs-5.0.1</code>
* <code>/usr/local/gromacs-5.1.1</code>

Script to source therein (assuming [https://en.wikipedia.org/wiki/Bash_(Unix_shell) bash]): <code>bin/GMXRC.bash</code>

Ana provided an [https://wiki.uni-due.de/vilaverde/index.php/File:Gromacs_cpu.sh example script] to be submitted via <code>sbatch</code>.

== OpenMolcas ==

(compiled with Intel compiler and MKL)

Minimal example script to be <code>sbatch</code>ed:

#!/bin/bash

export MOLCAS=/usr/local/openmolcas
export MOLCAS_WORKDIR=/tmp/$USER-$SLURM_JOB_NAME-$SLURM_JOB_ID
mkdir $MOLCAS_WORKDIR
export PATH=$PATH:$MOLCAS
export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/mkl/latest/lib/intel64
export OMP_NUM_THREADS=${SLURM_NTASKS:-1}

pymolcas the_input.inp

rm -rf $MOLCAS_WORKDIR

If you want/need to use the module system instead of setting <code>LD_LIBRARY_PATH</code> manually:

shopt -s expand_aliases
source /etc/profile.d/modules.sh

module use /opt/intel/oneapi/modulefiles
module -s load compiler/latest
module -s load mkl/latest

= Intel Compiler & Co. =

* is located in <code>/opt/intel/oneapi</code>
* must be made available via <code>module use /opt/intel/oneapi/modulefiles</code> (unless you include <code>/opt/intel/oneapi/modulefiles</code> in your <code>MODULEPATH</code>), then <code>module avail</code> lists the available modules.

= Backups =

A backup of the users' home directories is taken nightly. Users residing on <code>/home/stor1.lv0</code> actually have seven backups corresponding to the last 7 days in <code>/exports/lv0/snapshots/days.</code>$d$<code>/stor1/home/stor1.lv0/$USER</code> with $d\in\{0,\dots,6\}$.

Zeon

2022-02-18T14:41:38Z

Brendel: /* Intel oneAPI */ +pitfalls

= New Opterox-Login =

Server is <code>zeon.physik.uni-due.de</code>

= Queueing system = [https://slurm.schedmd.com/ Slurm] =

* <code>sinfo</code> shows overall load and available queues (''partitions'').
* <code>squeue</code> shows running jobs.
* simplest submission: <code>sbatch -n</code>''n'' ''script-name''
* <code>scancel</code> ''job-id'' kills job.

= Intel oneAPI =

Intel compilers, MKL and MPI are installed, must be selected via the [https://modules.readthedocs.io/en/latest module system]:

<code>module use /opt/intel/oneapi/modulefiles</code> (unless you include that directory in your <code>MODULEPATH</code>)

* <code>module avail</code> lists the installed modules, relevant are:
** compiler/latest → <code>ifort</code>, <code>icpc</code>, <code>icc</code>, ...
** mpi/latest → <code>mpirun</code>, <code>mpiifort</code>, <code>mpiicpc</code>, <code>mpiicc</code>, ...
** mkl/latest
* <code>module load</code> ... loads a module.

Inside a shell script (bash), you have to do <code>shopt -s expand_aliases</code> before being able to use the <code>module</code> command.

== Pitfalls ==

* <code>ifort</code>/<code>mpiifort</code>: When compiling with <code>-i8</code>, you also have to link with <code>-i8</code> (cf. also [https://www.intel.com/content/www/us/en/develop/documentation/mpi-developer-reference-linux/top/command-reference/compiler-commands/compilation-command-options.html manual]).

Zeon

2022-02-17T15:43:45Z

Brendel: /* Intel oneAPI */ load

Zeon

2022-02-17T15:39:14Z

Brendel: /* Intel oneAPI */ shopt

= New Opterox-Login =

Server is <code>zeon.physik.uni-due.de</code>

= Queueing system = [https://slurm.schedmd.com/ Slurm] =

* <code>sinfo</code> shows overall load and available queues (''partitions'').
* <code>squeue</code> shows running jobs.
* simplest submission: <code>sbatch -n</code>''n'' ''script-name''
* <code>scancel</code> ''job-id'' kills job.

= Intel oneAPI =

Intel compilers, MKL and MPI are installed, must be selected via the [https://modules.readthedocs.io/en/latest module system]:

<code>module use /opt/intel/oneapi/modulefiles</code> (unless you include that directory in your <code>MODULEPATH</code>)

* <code>module avail</code> lists the installed modules, relevant are:
** compiler/latest → <code>ifort</code>, <code>icpc</code>, <code>icc</code>, ...
** mpi/latest → <code>mpirun</code>, <code>mpiifort</code>, <code>mpiicpc</code>, <code>mpiicc</code>, ...
** mkl/latest

Inside a shell script (bash), you have to do <code>shopt -s expand_aliases</code> before being able to use the <code>module</code> command.

Zeon

2022-02-17T15:30:56Z

Brendel: neu