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subvaspmanT3000
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.TH SUBVASP 1 "13 NOVEMBER 2020" "subvasp 2.0" "User Commands"
.SH NAME
subvasp \- VASP submit script
.SH SYNOPSIS
.B subvasp
.RB [ "\-haklyYz" ]
.RB [ "\-j \fIJOB_ID" ]
.RB [ "\-m \fISIZE" ]
.RB [ "\-N \fINAME" ]
.RB [ "\-q \fIRESOURCE_REQUEST_LIST" ]
.RB [ "\-p \fICPUS" ]
.RB [ "\-f \fIPPN" ]
.RB [ "\-t \fITIME" ]
.RB [ "\-T \fITIME(in sec)" ]
.RB [ "\-v \fIVERSION" ]
.RB [ "\-w \fIDIRECTORY_PATH" ]
.B \-\-help
.SH DESCRIPTION
This manual page documents \fBsubvasp\fP, a submit script for VASP calculation with the input directory \fIDIRECTORY_PATH\fP.
.SS Options
.TP
.B \-h
Show help for subvasp script. You can also use \fB\-\-help\fR or only basename \fBsubvasp\fR without any arguments.
.TP
.B \-a
Shows the applied defaults for the current user. All further processing will be stopped.
.TP
.B \-j \fIJOB_ID
Specifies the \fIJOB_ID\fR of a job which must have finished before this job will start.
.PP
.RS
As special value the last character \[oq]@\[cq] is accepted and replaced by its own jobname.
This allows to submit several jobs which will be executed one after the other to make up a workflow,
when all are submitted with the same name. In combination with \[oq]\fB\-N\fR\ @\[cq]
it will make the workflow unqiue for each directory. To avoid that each job overwrites the output of
a former job due to having the same name, the usage of \[oq]\fB\-j\fR\ @\[cq] will also change the mode of output
operation from \[oq]overwrite\[cq] to \[oq]append\[cq].
.PP
Note for clusters running SGE: Any comma separated list of \fIJOB_ID\fR\[cq]s and/or
\fINAME\fR\[cq]s can be specified for \fIJOB_ID\fR too. \fINAME\fR can in addition be made up of an
expression to match several \fINAME\fR\[cq]s. For details see the man page of \fBsge_types\fR section
\fBMATCHING TYPES\fR. If both arguments to options \fB\-j\fR and \fB\-N\fR end with an \[oq]@\[cq], only
the part consisting of the assembled pathname instead of the full jobname will be used. This allows to
specify \[oq]subvasp\ \fB\-j\fR\ \[dq]*@\[dq]\ \fB-N\fR\ part5_@\ ...\[cq] to match all steps in the same
directory submitted before, while each has an unique prefix.
.RE
.TP
.B \-k
Keep the generated commandfile in ~/cmd. It will neither be
deleted, nor submitted.
.TP
.B \-l
List of vasp input files that will be copied to the scratch folder for qsub run. Choices are:
.ad l
.PP
.RS
.RS
.PD 0
.TP 12
.B INCAR, POSCAR, KPOINTS, POTCAR \fP(default)
.TP
.B INCAR, POSCAR, KPOINTS, POTCAR, WAVECAR, CHGCAR \fP(will switch on if -l option is provided)
.PD
.RE
.ad b
.RE
.TP
.B \-m \fISIZE
Request a queue with having at least \fISIZE\fR MB of memory per processor(/core) per node (pmem). PBS
will not allow your job to submit if you use more momemory than allowed RAM/process in each node of specified
queue. Subvasp script will also exit with error msg if memory managment is not satisfied.
The default is user dependent and will showup with the option \fB\-a\fP.
.TP
.B \-N \fINAME
By default the name of the calculation directory will be taken for the
name of the job also. If this is not convenient (or possible as the name
of the directory starts with a digit), you can force the job to get
a chosen \fINAME\fR of your own.
.PP
.RS
If this \fINAME\fR ends with a hash, it will be substituted with the
default name. E.g. \[oq]\fB-N\fR run_#\[cq] for the input directory \[oq]test\[cq] will result in
\[oq]run_test\[cq] as jobname.
.PP
If this \fINAME\fR ends with an \[oq]@\[cq], it will be substituted with the pathname
to the input directory while disregarding up to three top level directories which
are usually /home/$USER/\fISOME_DIRECTORY\fP.
.RE
.TP
.B \-q \fIRESOURCE_REQUEST_LIST\fR
Request special resources on the queueing system. You may specify more than
one request using a list of the form: \fIRESOURCE_REQUEST_LIST\fR=\fIRESOURCE_REQUEST\fR[,\fIRESOURCE_REQUEST\fR]*
.TP
.B \-p \fICPUS
If you specify the \fB-p\fR option, you can request a parallel execution of the job
with more than one CPU, which is the default.
.TP
.B \-f \fI PPN
If you specify the \fB-f\fR option, you can request a parallel execution of the job
with more than one core (no. of process or core per node), which is the default.
.TP
.B \-t \fITIME
Request a queue with a job time of \fITIME\fR hours. The value of \fITIME\fR can
have the format [\fIHOURS\fR]:\fIMINUTES\fR for finer adjustment. As special value
the case insensitive string \[oq]infinity\[cq] to request no time limit for this job
is also supported.
The default is user dependent and will showup with the option \fB\-a\fP.
.TP
.B \-T \fITIME
If time needed for cleaning and copying back is not enough due to a lot of
large files (e.g. WAVECAR, CHGCAR etc.) then use this option
to allocate more time for copying. The value of \fITIME\fR can only be in sec.
The default is 60 sec and will showup with the option \fB\-a\fP.
.TP
.B \-v \fIVERSION
Specifies, what executable should be used for the VASP job. The
available choices for \fIVERSION\fR are:
.ad l
.PP
.RS
.RS
.PD 0
.TP 12
.B 5.4.4+
VASP 5.4.4+ (default)
.TP
.B 5.4.4+-n
VASP 5.4.4+ compiled with NCL option
.TP
.B 5.4.4+-g
VASP 5.4.4+ compiled with \[*G]-point options (-DwNGXhalf, resp. -DwNGZhalf)
.TP
.B 5.4.4+c
VASP 5.4.4+ Lattice vector constrained in x, y direction
.TP
.B 5.4.4+c-n
VASP 5.4.4+ Lattice vector constrained in x, y direction compiled with NCL option
.TP
.B 5.4.4+c-g
VASP 5.4.4+ Lattice vector constrained in x, y direction compiled with \[*G]-point options (-DwNGXhalf, resp. -DwNGZhalf)
.PD
.RE
.ad b
.PP
These are self-compiled versions, compiled with the Intel Fortran Compiler.
.PP
.char \[el] \f[S]\N'188'\fP
.PP
The above specified built-in default version of the application might be overridden by setting the environment variable \fBVASP_VERSION\fR to any of the listed values. The effective default will show up with the option \fB\-a\fP.
.RE
.TP
.B \-w \fIDIRECTORY_PATH
By default the directory, for which the calculation will be made, is
the current working directory. By using this switch you can submit any
directory to the job. So the default behavior could be written like:
\[oq]\fB-w\fP .\[cq].
.TP
.B \-y
The output of the submission script is redirected to \[oq]stderr\[cq] and the only output
on \[oq]stdout\[cq] is the \fIJOB_ID\fR of the submitted job (unless used together with
the \fB\-Y\fR option). This allows easy assignment of the \fIJOB_ID\fR to a variable when
scripting the submission script. If \fB\-Y\fR is given too, \fIJOB_ID\fR and \fINAME\fR
will be output to \[oq]stdout\[cq] in this order, separated by a space character.
.TP
.B \-Y
The output of the submission script is redirected to \[oq]stderr\[cq] and the only output
on \[oq]stdout\[cq] is the \fINAME\fR of the submitted job (unless used together with
the \fB\-y\fR option). This allows easy assignment of the \fINAME\fR to a variable when
scripting the submission script. If \fB\-y\fR is given too, \fIJOB_ID\fR and \fINAME\fR
will be output to \[oq]stdout\[cq] in this order, separated by a space character.
.TP
.B \-z
Shows the processed option file(s) for the current user (see
.SM
.B FILES
below). All further processing will be stopped.
.TP
.B \-\-help
Show help for subvasp script. You can also use \fB\-h\fR or only basename \fBsubvasp\fR without any arguments.
.SH FILES
.TP
\fI$cwd/.subrc\fR
cwd default option file
.TP
\fI$HOME/.subrc\fR
user default option file
.TP
\fI<script_root>/subrc\fR
common default option file
.PP
Each line in these files may have options for the used submit scripts. First
in each line the name of the targeted submit script has to be specified, which
is the scriptname without the prefix \[oq]sub\[cq], hence a line might read like:
.PP
.RS
vasp -m 450 -N ExtraName -h
.RE
.PP
If an option line occurs multiple times for one type of submit script, then all
are read and processed one after the other.
.PP
All or some of the above mentioned option files may exist and are processed in
the reverse order.
.PP
Options given on the command line are processed last and may overwrite any of the
options in the option file.
.SH AUTHOR
Originally was written by Reuti <[email protected]>. Updated by --------.
.SH REPORTING BUGS
Report bugs to <[email protected]>.
.SH COPYRIGHT
Copyright \[co] 2020 Leipzig University Chemistry.
.br
This is free software. You may redistribute copies of it under the terms of the GNU General Public License
<http://www.gnu.org/licenses/gpl.html>. There is NO WARRANTY, to the extent permitted by law.
.SH "SEE ALSO"