mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-03 18:38:23 +01:00
GitHub
commit
618d4ca8b3
@ -143,7 +143,7 @@ IRPF90
|
||||
to Parameters (IRP) method.
|
||||
|
||||
* Download the latest version of IRPF90
|
||||
here : `<https://github.com/scemama/irpf90/releases/latest>`_ and move
|
||||
here : `<https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz>`_ and move
|
||||
the downloaded archive in the :file:`${QP_ROOT}/external` directory
|
||||
|
||||
* Extract the archive and go into the :file:`irpf90-*` directory to run
|
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|
||||
1
REPLACE
1
REPLACE
@ -834,3 +834,4 @@ qp_name potential_sr_c_alpha_ao_pbe --rename=potential_c_alpha_ao_sr_pbe
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||||
qp_name potential_sr_c_beta_ao_pbe --rename=potential_c_beta_ao_sr_pbe
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||||
qp_name potential_sr_xc_alpha_ao_pbe --rename=potential_xc_alpha_ao_sr_pbe
|
||||
qp_name potential_sr_xc_beta_ao_pbe --rename=potential_xc_beta_ao_sr_pbe
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qp_name disk_access_nuclear_repulsion --rename=io_nuclear_repulsion
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@ -1,71 +0,0 @@
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#!/usr/bin/env python2
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||||
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||||
"""
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Creates an ssh tunnel for using slaves on another network.
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Launch a server on the front-end node of the cluster on which the master
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process runs. Then start a client ont the front-end node of the distant
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cluster.
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Usage:
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qp_tunnel server EZFIO_DIR
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qp_tunnel client <address> EZFIO_DIR
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Options:
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-h --help
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"""
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import os
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import sys
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import zmq
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try:
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import qp_path
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except ImportError:
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print "source .quantum_package.rc"
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raise
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from docopt import docopt
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from ezfio import ezfio
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def get_address(filename):
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with open(os.path.join(filename,'work','qp_run_address'),'r') as f:
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a = f.readlines()[0].strip()
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return a
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def set_address(filename,address):
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with open(os.path.join(filename,'work','qp_run_address'),'r') as f:
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backup = f.readlines()
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with open(os.path.join(filename,'work','qp_run_address'),'w') as f:
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f.write('\n'.join([address]+backup))
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|
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def main_server(arguments,filename):
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destination = get_address(filename)
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print destination
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def main_client(arguments,filename):
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destination = arguments["<address>"]
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print destination
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def main(arguments):
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"""Main function"""
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print arguments
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filename = arguments["EZFIO_DIR"]
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|
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if arguments["server"]:
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return main_server(arguments, filename)
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if arguments["client"]:
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return main_client(arguments, filename)
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if __name__ == '__main__':
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ARGUMENTS = docopt(__doc__)
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main(ARGUMENTS)
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12
configure
vendored
12
configure
vendored
@ -438,18 +438,18 @@ if [[ ${ZLIB} = $(not_found) ]] ; then
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fail
|
||||
fi
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|
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BWRAP=$(find_exe bwrap)
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||||
if [[ ${BWRAP} = $(not_found) ]] ; then
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error "Bubblewrap (bwrap) is not installed."
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||||
fail
|
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fi
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|
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LIBCAP=$(find_lib -lcap)
|
||||
if [[ ${LIBCAP} = $(not_found) ]] ; then
|
||||
error "Libcap (libcap) is not installed."
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||||
fail
|
||||
fi
|
||||
|
||||
BWRAP=$(find_exe bwrap)
|
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if [[ ${BWRAP} = $(not_found) ]] ; then
|
||||
error "Bubblewrap (bwrap) is not installed."
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||||
fail
|
||||
fi
|
||||
|
||||
OPAM=$(find_exe opam)
|
||||
if [[ ${OPAM} = $(not_found) ]] ; then
|
||||
error "OPAM (ocaml) package manager is not installed."
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|
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BIN
data/qp2.png
BIN
data/qp2.png
Binary file not shown.
|
Before Width: | Height: | Size: 5.9 MiB After Width: | Height: | Size: 351 KiB |
BIN
data/qp2_hd.png
Normal file
BIN
data/qp2_hd.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 5.9 MiB |
89
docs/source/users_guide/qp_tunnel.rst
Normal file
89
docs/source/users_guide/qp_tunnel.rst
Normal file
@ -0,0 +1,89 @@
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||||
.. _qp_tunnel:
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||||
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||||
=========
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||||
qp_tunnel
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||||
=========
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||||
|
||||
.. TODO
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||||
|
||||
.. program:: qp_tunnel
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||||
|
||||
Establishes a tunnel to allow communications between machines within
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||||
different networks, for example multiple MPI slave jobs running on
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||||
different clusters.
|
||||
|
||||
|
||||
Usage
|
||||
-----
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||||
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.. code:: bash
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||||
|
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qp_tunnel [-g] (ADDRESS|EZFIO_DIR)
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|
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``EZFIO_DIR`` is the name of the |EZFIO| directory containing the data,
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and ``ADDRESS`` is the address of another tunnel.
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||||
|
||||
|
||||
.. option:: -h, --help
|
||||
|
||||
Displays the help message
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||||
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|
||||
.. option:: -g, --get-input
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||||
|
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Download the EZFIO directory from the remote instance of qp_tunnel.
|
||||
|
||||
|
||||
Example
|
||||
-------
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||||
|
||||
.. code:: text
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||||
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||||
+-------------------+ +------------------+
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||||
| | | |
|
||||
| N1_1 N1_2 N1_3 | | N2_1 N2_2 N2_3 |
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||||
| | | | | | | | | |
|
||||
| +----+----+ | | +----+----+ |
|
||||
| | | | | |
|
||||
| C1 F1 | | F2 C2 |
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||||
| +---------=----=--------+ |
|
||||
| | | |
|
||||
+-------------------+ +------------------+
|
||||
|
||||
|
||||
Imagine you have two clusters, C1 and C2. Each cluster is accessible via SSH
|
||||
on a front-end named respectively F1 and F2. Groups of nodes N1 and N2 have
|
||||
been reserved by the batch scheduling system on both clusters.
|
||||
Each node in N1 is on the same network as the other nodes of N1, but they
|
||||
can't access the network on which the nodes of N2 are.
|
||||
|
||||
1) Start a parallel simulation on the cluster C1, running on nodes N1.
|
||||
We assume that there is a shared file system, such that F1 can access
|
||||
the EZFIO directory. We also assume that F1 can communicate with the
|
||||
nodes of N1.
|
||||
|
||||
2) Run a tunnel on the front-end F1 and keep it running:
|
||||
|
||||
.. code:: bash
|
||||
|
||||
me@f1 $ qp_tunnel my_directory.ezfio
|
||||
Connect to:
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||||
tcp://31.122.230.47:42379
|
||||
Ready
|
||||
|
||||
3) On the front-end F2, run another instance connecting to the other one,
|
||||
which will fetch the |EZFIO| directory:
|
||||
|
||||
.. code:: bash
|
||||
|
||||
me@f2 $ qp_tunnel --get-input tcp://31.122.230.47:42379
|
||||
Connect to:
|
||||
tcp://31.122.209.139:42379
|
||||
Communication [ OK ]
|
||||
Getting input... my_directory.ezfio ...done
|
||||
Ready
|
||||
|
||||
4) Keep the tunnel running, and you can now run a slave simulation within the
|
||||
nodes N2.
|
||||
|
||||
|
||||
139
man/qp_tunnel.1
Normal file
139
man/qp_tunnel.1
Normal file
@ -0,0 +1,139 @@
|
||||
.\" Man page generated from reStructuredText.
|
||||
.
|
||||
.TH "QP_TUNNEL" "1" "Jun 15, 2019" "2.0" "Quantum Package"
|
||||
.SH NAME
|
||||
qp_tunnel \- | Quantum Package >
|
||||
.
|
||||
.nr rst2man-indent-level 0
|
||||
.
|
||||
.de1 rstReportMargin
|
||||
\\$1 \\n[an-margin]
|
||||
level \\n[rst2man-indent-level]
|
||||
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
-
|
||||
\\n[rst2man-indent0]
|
||||
\\n[rst2man-indent1]
|
||||
\\n[rst2man-indent2]
|
||||
..
|
||||
.de1 INDENT
|
||||
.\" .rstReportMargin pre:
|
||||
. RS \\$1
|
||||
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
|
||||
. nr rst2man-indent-level +1
|
||||
.\" .rstReportMargin post:
|
||||
..
|
||||
.de UNINDENT
|
||||
. RE
|
||||
.\" indent \\n[an-margin]
|
||||
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.nr rst2man-indent-level -1
|
||||
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
|
||||
..
|
||||
.sp
|
||||
Establishes a tunnel to allow communications between machines within
|
||||
different networks, for example multiple MPI slave jobs running on
|
||||
different clusters.
|
||||
.SH USAGE
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
qp_tunnel [\-g] (ADDRESS|EZFIO_DIR)
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.sp
|
||||
\fBEZFIO_DIR\fP is the name of the \fI\%EZFIO\fP directory containing the data,
|
||||
and \fBADDRESS\fP is the address of another tunnel.
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-h, \-\-help
|
||||
Displays the help message
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.TP
|
||||
.B \-g, \-\-get\-input
|
||||
Download the EZFIO directory from the remote instance of qp_tunnel.
|
||||
.UNINDENT
|
||||
.SH EXAMPLE
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
+\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+ +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+
|
||||
| | | |
|
||||
| N1_1 N1_2 N1_3 | | N2_1 N2_2 N2_3 |
|
||||
| | | | | | | | | |
|
||||
| +\-\-\-\-+\-\-\-\-+ | | +\-\-\-\-+\-\-\-\-+ |
|
||||
| | | | | |
|
||||
| C1 F1 | | F2 C2 |
|
||||
| +\-\-\-\-\-\-\-\-\-=\-\-\-\-=\-\-\-\-\-\-\-\-+ |
|
||||
| | | |
|
||||
+\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+ +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.sp
|
||||
Imagine you have two clusters, C1 and C2. Each cluster is accessible via SSH
|
||||
on a front\-end named respectively F1 and F2. Groups of nodes N1 and N2 have
|
||||
been reserved by the batch scheduling system on both clusters.
|
||||
Each node in N1 is on the same network as the other nodes of N1, but they
|
||||
can’t access the network on which the nodes of N2 are.
|
||||
.INDENT 0.0
|
||||
.IP 1. 3
|
||||
Start a parallel simulation on the cluster C1, running on nodes N1.
|
||||
We assume that there is a shared file system, such that F1 can access
|
||||
the EZFIO directory. We also assume that F1 can communicate with the
|
||||
nodes of N1.
|
||||
.IP 2. 3
|
||||
Run a tunnel on the front\-end F1 and keep it running:
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
me@f1 $ qp_tunnel my_directory.ezfio
|
||||
Connect to:
|
||||
tcp://31.122.230.47:42379
|
||||
Ready
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.IP 3. 3
|
||||
On the front\-end F2, run another instance connecting to the other one,
|
||||
which will fetch the \fI\%EZFIO\fP directory:
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
.sp
|
||||
.nf
|
||||
.ft C
|
||||
me@f2 $ qp_tunnel \-\-get\-input tcp://31.122.230.47:42379
|
||||
Connect to:
|
||||
tcp://31.122.209.139:42379
|
||||
Communication [ OK ]
|
||||
Getting input... my_directory.ezfio ...done
|
||||
Ready
|
||||
.ft P
|
||||
.fi
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.INDENT 0.0
|
||||
.IP 4. 3
|
||||
Keep the tunnel running, and you can now run a slave simulation within the
|
||||
nodes N2.
|
||||
.UNINDENT
|
||||
.SH AUTHOR
|
||||
A. Scemama, E. Giner
|
||||
.SH COPYRIGHT
|
||||
2019, A. Scemama, E. Giner
|
||||
.\" Generated by docutils manpage writer.
|
||||
.
|
||||
@ -34,7 +34,7 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.INDENT 3.5
|
||||
Rotates molecular orbitals i and j by combining them as
|
||||
$1/sqrt{2} ( phi_i + phi_j )$ and
|
||||
$1/sqrt{2} ( phi_i \- phi_j )$.
|
||||
$1/sqrt{2} ( phi_i - phi_j )$.
|
||||
.sp
|
||||
Needs:
|
||||
.INDENT 0.0
|
||||
|
||||
55
man/test.1
Normal file
55
man/test.1
Normal file
@ -0,0 +1,55 @@
|
||||
.\" Man page generated from reStructuredText.
|
||||
.
|
||||
.TH "TEST" "1" "Jun 15, 2019" "2.0" "Quantum Package"
|
||||
.SH NAME
|
||||
test \- | Quantum Package >
|
||||
.
|
||||
.nr rst2man-indent-level 0
|
||||
.
|
||||
.de1 rstReportMargin
|
||||
\\$1 \\n[an-margin]
|
||||
level \\n[rst2man-indent-level]
|
||||
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
-
|
||||
\\n[rst2man-indent0]
|
||||
\\n[rst2man-indent1]
|
||||
\\n[rst2man-indent2]
|
||||
..
|
||||
.de1 INDENT
|
||||
.\" .rstReportMargin pre:
|
||||
. RS \\$1
|
||||
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
|
||||
. nr rst2man-indent-level +1
|
||||
.\" .rstReportMargin post:
|
||||
..
|
||||
.de UNINDENT
|
||||
. RE
|
||||
.\" indent \\n[an-margin]
|
||||
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.nr rst2man-indent-level -1
|
||||
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
|
||||
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
|
||||
..
|
||||
.INDENT 0.0
|
||||
.INDENT 3.5
|
||||
Calls:
|
||||
.INDENT 0.0
|
||||
.INDENT 2.0
|
||||
.IP \(bu 2
|
||||
\fBtwo_e_integrals_index()\fP
|
||||
.UNINDENT
|
||||
.INDENT 2.0
|
||||
.IP \(bu 2
|
||||
\fBtwo_e_integrals_index_reverse()\fP
|
||||
.UNINDENT
|
||||
.INDENT 2.0
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.UNINDENT
|
||||
.SH AUTHOR
|
||||
A. Scemama, E. Giner
|
||||
.SH COPYRIGHT
|
||||
2019, A. Scemama, E. Giner
|
||||
.\" Generated by docutils manpage writer.
|
||||
.
|
||||
@ -1,4 +1,4 @@
|
||||
PKG core ZMQ cryptokit
|
||||
PKG core zmq cryptokit
|
||||
B _build/
|
||||
|
||||
|
||||
|
||||
214
ocaml/Bitlist.ml
214
ocaml/Bitlist.ml
@ -7,82 +7,61 @@ Type for bits strings
|
||||
list of Bits
|
||||
*)
|
||||
|
||||
type t = Bit.t list
|
||||
type t = int64 array
|
||||
|
||||
|
||||
let n_int = Array.length
|
||||
|
||||
(* Create a zero bit list *)
|
||||
let zero n_int =
|
||||
Array.make (N_int_number.to_int n_int) 0L
|
||||
|
||||
(* String representation *)
|
||||
let to_string b =
|
||||
let rec do_work accu = function
|
||||
| [] -> accu
|
||||
| head :: tail ->
|
||||
let new_accu = (Bit.to_string head) ^ accu
|
||||
in do_work new_accu tail
|
||||
let int64_to_string x =
|
||||
String.init 64 (fun i ->
|
||||
if Int64.logand x @@ Int64.shift_left 1L i <> 0L then
|
||||
'+'
|
||||
else
|
||||
'-')
|
||||
in
|
||||
do_work "" b
|
||||
Array.map int64_to_string b
|
||||
|> Array.to_list
|
||||
|> String.concat ""
|
||||
|
||||
|
||||
let of_string ?(zero='0') ?(one='1') s =
|
||||
List.init (String.length s) (String.get s)
|
||||
|> List.rev_map ( fun c ->
|
||||
if (c = zero) then Bit.Zero
|
||||
else if (c = one) then Bit.One
|
||||
else (failwith ("Error in bitstring ") ) )
|
||||
let n_int = ( (String.length s - 1) lsr 6 ) + 1 in
|
||||
let result = Array.make n_int 0L in
|
||||
String.iteri (fun i c ->
|
||||
if c = one then
|
||||
begin
|
||||
let iint = i lsr 6 in (* i / 64 *)
|
||||
let k = i - (iint lsl 6) in
|
||||
result.(iint) <- Int64.logor result.(iint) @@ Int64.shift_left 1L k;
|
||||
end) s;
|
||||
result
|
||||
|
||||
let of_string_mp s =
|
||||
List.init (String.length s) (String.get s)
|
||||
|> List.rev_map (function
|
||||
| '-' -> Bit.Zero
|
||||
| '+' -> Bit.One
|
||||
| _ -> failwith ("Error in bitstring ") )
|
||||
let of_string_mp = of_string ~zero:'-' ~one:'+'
|
||||
|
||||
|
||||
(* Create a bit list from an int64 *)
|
||||
let of_int64 i =
|
||||
|
||||
let rec do_work accu = function
|
||||
| 0L -> Bit.Zero :: accu |> List.rev
|
||||
| 1L -> Bit.One :: accu |> List.rev
|
||||
| i ->
|
||||
let b =
|
||||
match (Int64.logand i 1L ) with
|
||||
| 0L -> Bit.Zero
|
||||
| 1L -> Bit.One
|
||||
| _ -> raise (Failure "i land 1 not in (0,1)")
|
||||
in
|
||||
do_work (b :: accu) (Int64.shift_right_logical i 1)
|
||||
in
|
||||
|
||||
let adjust_length result =
|
||||
let rec do_work accu = function
|
||||
| 64 -> List.rev accu
|
||||
| i when i>64 -> raise (Failure "Error in of_int64 > 64")
|
||||
| i when i<0 -> raise (Failure "Error in of_int64 < 0")
|
||||
| i -> do_work (Bit.Zero :: accu) (i+1)
|
||||
in
|
||||
do_work (List.rev result) (List.length result)
|
||||
in
|
||||
adjust_length (do_work [] i)
|
||||
|
||||
let of_int64 i = [| i |]
|
||||
|
||||
(* Create an int64 from a bit list *)
|
||||
let to_int64 l =
|
||||
assert ( (List.length l) <= 64) ;
|
||||
let rec do_work accu = function
|
||||
| [] -> accu
|
||||
| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
|
||||
| Bit.One::tail -> do_work Int64.(logor one (shift_left accu 1)) tail
|
||||
in do_work Int64.zero (List.rev l)
|
||||
let to_int64 = function
|
||||
| [| i |] -> i
|
||||
| _ -> failwith "N_int > 1"
|
||||
|
||||
|
||||
(* Create a bit list from a list of int64 *)
|
||||
let of_int64_list l =
|
||||
List.map of_int64 l
|
||||
|> List.concat
|
||||
|
||||
(* Create a bit list from an array of int64 *)
|
||||
let of_int64_array l =
|
||||
Array.map of_int64 l
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
external of_int64_array : int64 array -> t = "%identity"
|
||||
external to_int64_array : t -> int64 array = "%identity"
|
||||
|
||||
|
||||
(* Create a bit list from a list of int64 *)
|
||||
let of_int64_list l =
|
||||
Array.of_list l |> of_int64_array
|
||||
|
||||
|
||||
(* Compute n_int *)
|
||||
@ -91,101 +70,64 @@ let n_int_of_mo_num mo_num =
|
||||
N_int_number.of_int ( (mo_num-1)/bit_kind_size + 1 )
|
||||
|
||||
|
||||
(* Create a zero bit list *)
|
||||
let zero n_int =
|
||||
let n_int = N_int_number.to_int n_int in
|
||||
let a = Array.init n_int (fun i-> 0L) in
|
||||
of_int64_list ( Array.to_list a )
|
||||
|
||||
|
||||
(* Create an int64 list from a bit list *)
|
||||
let to_int64_list l =
|
||||
let rec do_work accu buf counter = function
|
||||
| [] ->
|
||||
begin
|
||||
match buf with
|
||||
| [] -> accu
|
||||
| _ -> (List.rev buf)::accu
|
||||
end
|
||||
| i::tail ->
|
||||
if (counter < 64) then
|
||||
do_work accu (i::buf) (counter+1) tail
|
||||
else
|
||||
do_work ( (List.rev (i::buf))::accu) [] 1 tail
|
||||
in
|
||||
let l = do_work [] [] 1 l
|
||||
in
|
||||
List.rev_map to_int64 l
|
||||
to_int64_array l |> Array.to_list
|
||||
|
||||
(* Create an array of int64 from a bit list *)
|
||||
let to_int64_array l =
|
||||
to_int64_list l
|
||||
|> Array.of_list
|
||||
|
||||
(* Create a bit list from a list of MO indices *)
|
||||
let of_mo_number_list n_int l =
|
||||
let n_int = N_int_number.to_int n_int in
|
||||
let length = n_int*64 in
|
||||
let a = Array.make length (Bit.Zero) in
|
||||
List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
|
||||
Array.to_list a
|
||||
let result = zero n_int in
|
||||
List.iter (fun j ->
|
||||
let i = (MO_number.to_int j) - 1 in
|
||||
let iint = i lsr 6 in (* i / 64 *)
|
||||
let k = i - (iint lsl 6) in
|
||||
result.(iint) <- Int64.logor result.(iint) @@ Int64.shift_left 1L k;
|
||||
) l;
|
||||
result
|
||||
|
||||
|
||||
let to_mo_number_list l =
|
||||
let a = Array.of_list l in
|
||||
let mo_num = MO_number.get_max () in
|
||||
let rec do_work accu = function
|
||||
| 0 -> accu
|
||||
| i ->
|
||||
begin
|
||||
let new_accu =
|
||||
match a.(i-1) with
|
||||
| Bit.One -> (MO_number.of_int ~max:mo_num i)::accu
|
||||
| Bit.Zero -> accu
|
||||
in
|
||||
do_work new_accu (i-1)
|
||||
end
|
||||
let rec aux_one x shift accu = function
|
||||
| -1 -> accu
|
||||
| i -> if Int64.logand x (Int64.shift_left 1L i) <> 0L then
|
||||
aux_one x shift ( (i+shift) ::accu) (i-1)
|
||||
else
|
||||
aux_one x shift accu (i-1)
|
||||
in
|
||||
do_work [] (List.length l)
|
||||
|
||||
Array.mapi (fun i x ->
|
||||
let shift = (i lsr 6) lsl 6 + 1 in
|
||||
aux_one x shift [] 63
|
||||
) l
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
|> List.map MO_number.of_int
|
||||
|
||||
|
||||
|
||||
(* logical operations on bit_list *)
|
||||
let logical_operator2 op a b =
|
||||
let rec do_work_binary result a b =
|
||||
match a, b with
|
||||
| [], [] -> result
|
||||
| [], _ | _ , [] -> raise (Failure "Lists should have same length")
|
||||
| (ha::ta), (hb::tb) ->
|
||||
let newbit = op ha hb
|
||||
in do_work_binary (newbit::result) ta tb
|
||||
let and_operator a b = Array.map2 Int64.logand a b
|
||||
let xor_operator a b = Array.map2 Int64.logxor a b
|
||||
let or_operator a b = Array.map2 Int64.logor a b
|
||||
let not_operator b = Array.map Int64.lognot b
|
||||
|
||||
|
||||
|
||||
let pop_sign =
|
||||
let mask =
|
||||
(Int64.pred (Int64.shift_left 1L 63))
|
||||
in
|
||||
List.rev (do_work_binary [] a b)
|
||||
|
||||
|
||||
let logical_operator1 op b =
|
||||
let rec do_work_unary result b =
|
||||
match b with
|
||||
| [] -> result
|
||||
| (hb::tb) ->
|
||||
let newbit = op hb
|
||||
in do_work_unary (newbit::result) tb
|
||||
in
|
||||
List.rev (do_work_unary [] b)
|
||||
|
||||
|
||||
let and_operator a b = logical_operator2 Bit.and_operator a b
|
||||
let xor_operator a b = logical_operator2 Bit.xor_operator a b
|
||||
let or_operator a b = logical_operator2 Bit.or_operator a b
|
||||
let not_operator b = logical_operator1 Bit.not_operator b
|
||||
fun x -> Int64.logand mask x
|
||||
|
||||
|
||||
let popcnt b =
|
||||
List.fold_left (fun accu -> function
|
||||
| Bit.One -> accu+1
|
||||
| Bit.Zero -> accu
|
||||
) 0 b
|
||||
Array.fold_left (fun accu x ->
|
||||
if x >= 0L then
|
||||
accu + (Z.popcount @@ Z.of_int64 x)
|
||||
else
|
||||
accu + 1 + (Z.popcount @@ Z.of_int64 (pop_sign x))
|
||||
) 0 b
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
type t = Bit.t list
|
||||
type t
|
||||
|
||||
(** The zero bit list *)
|
||||
val zero : Qptypes.N_int_number.t -> t
|
||||
|
||||
@ -25,19 +25,6 @@ let to_bitlist_couple x =
|
||||
in (xa,xb)
|
||||
|
||||
|
||||
let bitlist_to_string ~mo_num x =
|
||||
let len =
|
||||
MO_number.to_int mo_num
|
||||
in
|
||||
let s =
|
||||
List.map (function
|
||||
| Bit.Zero -> "-"
|
||||
| Bit.One -> "+"
|
||||
) x
|
||||
|> String.concat ""
|
||||
in
|
||||
String.sub s 0 len
|
||||
|
||||
|
||||
|
||||
let of_int64_array ~n_int ~alpha ~beta x =
|
||||
@ -48,37 +35,29 @@ let of_int64_array ~n_int ~alpha ~beta x =
|
||||
in
|
||||
if ( (Bitlist.popcnt a) <> alpha) then
|
||||
begin
|
||||
let mo_num = MO_number.get_max () in
|
||||
let mo_num = MO_number.of_int mo_num ~max:mo_num in
|
||||
failwith (Printf.sprintf "Expected %d electrons in alpha determinant
|
||||
%s" alpha (bitlist_to_string ~mo_num:mo_num a) )
|
||||
%s" alpha (Bitlist.to_string a) )
|
||||
end;
|
||||
if ( (Bitlist.popcnt b) <> beta ) then
|
||||
begin
|
||||
let mo_num = MO_number.get_max () in
|
||||
let mo_num = MO_number.of_int mo_num ~max:mo_num in
|
||||
failwith (Printf.sprintf "Expected %d electrons in beta determinant
|
||||
%s" beta (bitlist_to_string ~mo_num:mo_num b) )
|
||||
%s" beta (Bitlist.to_string b) )
|
||||
end;
|
||||
x
|
||||
|
||||
|
||||
let of_bitlist_couple ?n_int ~alpha ~beta (xa,xb) =
|
||||
let of_bitlist_couple ~n_int ~alpha ~beta (xa,xb) =
|
||||
let ba, bb =
|
||||
Bitlist.to_int64_array xa ,
|
||||
Bitlist.to_int64_array xb
|
||||
and n_int =
|
||||
match n_int with
|
||||
| Some x -> x
|
||||
| None -> Bitlist.n_int_of_mo_num (List.length xa)
|
||||
in
|
||||
of_int64_array ~n_int ~alpha ~beta (Array.concat [ba;bb])
|
||||
|
||||
|
||||
let to_string ~mo_num x =
|
||||
let (xa,xb) = to_bitlist_couple x in
|
||||
[ " " ; bitlist_to_string ~mo_num xa ; "\n" ;
|
||||
" " ; bitlist_to_string ~mo_num xb ]
|
||||
[ " " ; Bitlist.to_string xa ; "\n" ;
|
||||
" " ; Bitlist.to_string xb ]
|
||||
|> String.concat ""
|
||||
|
||||
|
||||
|
||||
@ -24,7 +24,7 @@ val to_alpha_beta : t -> (int64 array)*(int64 array)
|
||||
val to_bitlist_couple : t -> Bitlist.t * Bitlist.t
|
||||
|
||||
(** Create from a bit list *)
|
||||
val of_bitlist_couple : ?n_int:Qptypes.N_int_number.t ->
|
||||
val of_bitlist_couple : n_int:Qptypes.N_int_number.t ->
|
||||
alpha:Qptypes.Elec_alpha_number.t ->
|
||||
beta:Qptypes.Elec_beta_number.t ->
|
||||
Bitlist.t * Bitlist.t -> t
|
||||
|
||||
@ -7,14 +7,14 @@ module Determinants_by_hand : sig
|
||||
{ n_int : N_int_number.t;
|
||||
bit_kind : Bit_kind.t;
|
||||
n_det : Det_number.t;
|
||||
n_det_qp_edit : Det_number.t;
|
||||
n_states : States_number.t;
|
||||
expected_s2 : Positive_float.t;
|
||||
psi_coef : Det_coef.t array;
|
||||
psi_det : Determinant.t array;
|
||||
state_average_weight : Positive_float.t array;
|
||||
} [@@deriving sexp]
|
||||
val read : unit -> t
|
||||
val read_maybe : unit -> t option
|
||||
val read : ?full:bool -> unit -> t option
|
||||
val write : t -> unit
|
||||
val to_string : t -> string
|
||||
val to_rst : t -> Rst_string.t
|
||||
@ -28,6 +28,7 @@ end = struct
|
||||
{ n_int : N_int_number.t;
|
||||
bit_kind : Bit_kind.t;
|
||||
n_det : Det_number.t;
|
||||
n_det_qp_edit : Det_number.t;
|
||||
n_states : States_number.t;
|
||||
expected_s2 : Positive_float.t;
|
||||
psi_coef : Det_coef.t array;
|
||||
@ -38,8 +39,6 @@ end = struct
|
||||
|
||||
let get_default = Qpackage.get_ezfio_default "determinants";;
|
||||
|
||||
let n_det_read_max = 10_000 ;;
|
||||
|
||||
let read_n_int () =
|
||||
if not (Ezfio.has_determinants_n_int()) then
|
||||
Ezfio.get_mo_basis_mo_num ()
|
||||
@ -80,11 +79,27 @@ end = struct
|
||||
|> Det_number.of_int
|
||||
;;
|
||||
|
||||
let read_n_det_qp_edit () =
|
||||
if not (Ezfio.has_determinants_n_det_qp_edit ()) then
|
||||
begin
|
||||
let n_det = read_n_det () |> Det_number.to_int in
|
||||
Ezfio.set_determinants_n_det_qp_edit n_det
|
||||
end;
|
||||
Ezfio.get_determinants_n_det_qp_edit ()
|
||||
|> Det_number.of_int
|
||||
;;
|
||||
|
||||
let write_n_det n =
|
||||
Det_number.to_int n
|
||||
|> Ezfio.set_determinants_n_det
|
||||
;;
|
||||
|
||||
let write_n_det_qp_edit n =
|
||||
let n_det = read_n_det () |> Det_number.to_int in
|
||||
min n_det (Det_number.to_int n)
|
||||
|> Ezfio.set_determinants_n_det_qp_edit
|
||||
;;
|
||||
|
||||
let read_n_states () =
|
||||
if not (Ezfio.has_determinants_n_states ()) then
|
||||
Ezfio.set_determinants_n_states 1
|
||||
@ -178,7 +193,7 @@ end = struct
|
||||
|> Ezfio.set_determinants_expected_s2
|
||||
;;
|
||||
|
||||
let read_psi_coef () =
|
||||
let read_psi_coef ~read_only () =
|
||||
if not (Ezfio.has_determinants_psi_coef ()) then
|
||||
begin
|
||||
let n_states =
|
||||
@ -189,7 +204,12 @@ end = struct
|
||||
~data:(List.init n_states (fun i -> if (i=0) then 1. else 0. ))
|
||||
|> Ezfio.set_determinants_psi_coef
|
||||
end;
|
||||
Ezfio.get_determinants_psi_coef ()
|
||||
begin
|
||||
if read_only then
|
||||
Ezfio.get_determinants_psi_coef_qp_edit ()
|
||||
else
|
||||
Ezfio.get_determinants_psi_coef ()
|
||||
end
|
||||
|> Ezfio.flattened_ezfio
|
||||
|> Array.map Det_coef.of_float
|
||||
;;
|
||||
@ -202,12 +222,15 @@ end = struct
|
||||
and n_states =
|
||||
States_number.to_int n_states
|
||||
in
|
||||
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
|
||||
|> Ezfio.set_determinants_psi_coef
|
||||
let r =
|
||||
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
|
||||
in
|
||||
Ezfio.set_determinants_psi_coef r;
|
||||
Ezfio.set_determinants_psi_coef_qp_edit r
|
||||
;;
|
||||
|
||||
|
||||
let read_psi_det () =
|
||||
let read_psi_det ~read_only () =
|
||||
let n_int = read_n_int ()
|
||||
and n_alpha = Ezfio.get_electrons_elec_alpha_num ()
|
||||
|> Elec_alpha_number.of_int
|
||||
@ -233,13 +256,21 @@ end = struct
|
||||
|> Ezfio.set_determinants_psi_det ;
|
||||
end ;
|
||||
let n_int = N_int_number.to_int n_int in
|
||||
let psi_det_array = Ezfio.get_determinants_psi_det () in
|
||||
let psi_det_array =
|
||||
if read_only then
|
||||
Ezfio.get_determinants_psi_det_qp_edit ()
|
||||
else
|
||||
Ezfio.get_determinants_psi_det ()
|
||||
in
|
||||
let dim = psi_det_array.Ezfio.dim
|
||||
and data = Ezfio.flattened_ezfio psi_det_array
|
||||
in
|
||||
assert (n_int = dim.(0));
|
||||
assert (dim.(1) = 2);
|
||||
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
|
||||
if read_only then
|
||||
assert (dim.(2) = (Det_number.to_int (read_n_det_qp_edit ())))
|
||||
else
|
||||
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
|
||||
Array.init dim.(2) (fun i ->
|
||||
Array.sub data (2*n_int*i) (2*n_int) )
|
||||
|> Array.map (Determinant.of_int64_array
|
||||
@ -252,40 +283,45 @@ end = struct
|
||||
|> Array.concat
|
||||
|> Array.to_list
|
||||
in
|
||||
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[| N_int_number.to_int n_int ; 2 ; Det_number.to_int n_det |] ~data:data
|
||||
|> Ezfio.set_determinants_psi_det
|
||||
let r =
|
||||
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[| N_int_number.to_int n_int ; 2 ; Det_number.to_int n_det |] ~data:data
|
||||
in
|
||||
Ezfio.set_determinants_psi_det r;
|
||||
Ezfio.set_determinants_psi_det_qp_edit r
|
||||
;;
|
||||
|
||||
|
||||
let read () =
|
||||
let read ?(full=true) () =
|
||||
|
||||
let n_det_qp_edit = read_n_det_qp_edit () in
|
||||
let n_det = read_n_det () in
|
||||
let read_only =
|
||||
if full then false else n_det_qp_edit <> n_det
|
||||
in
|
||||
|
||||
if (Ezfio.has_mo_basis_mo_num ()) then
|
||||
try
|
||||
Some
|
||||
{ n_int = read_n_int () ;
|
||||
bit_kind = read_bit_kind () ;
|
||||
n_det = read_n_det () ;
|
||||
n_det_qp_edit = read_n_det_qp_edit () ;
|
||||
expected_s2 = read_expected_s2 () ;
|
||||
psi_coef = read_psi_coef () ;
|
||||
psi_det = read_psi_det () ;
|
||||
psi_coef = read_psi_coef ~read_only () ;
|
||||
psi_det = read_psi_det ~read_only () ;
|
||||
n_states = read_n_states () ;
|
||||
state_average_weight = read_state_average_weight () ;
|
||||
}
|
||||
with _ -> None
|
||||
else
|
||||
failwith "No molecular orbitals, so no determinants"
|
||||
;;
|
||||
|
||||
let read_maybe () =
|
||||
let n_det =
|
||||
read_n_det ()
|
||||
in
|
||||
if ( (Det_number.to_int n_det) < n_det_read_max ) then
|
||||
try Some (read ()) with
|
||||
| Failure _ -> None
|
||||
else
|
||||
(* No molecular orbitals, so no determinants *)
|
||||
None
|
||||
;;
|
||||
|
||||
let write { n_int ;
|
||||
bit_kind ;
|
||||
n_det ;
|
||||
n_det_qp_edit ;
|
||||
expected_s2 ;
|
||||
psi_coef ;
|
||||
psi_det ;
|
||||
@ -297,9 +333,13 @@ end = struct
|
||||
write_n_det n_det;
|
||||
write_n_states n_states;
|
||||
write_expected_s2 expected_s2;
|
||||
write_psi_coef ~n_det:n_det ~n_states:n_states psi_coef ;
|
||||
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
|
||||
write_state_average_weight state_average_weight;
|
||||
if n_det <= n_det_qp_edit then
|
||||
begin
|
||||
write_n_det_qp_edit n_det;
|
||||
write_psi_coef ~n_det:n_det ~n_states:n_states psi_coef ;
|
||||
write_psi_det ~n_int:n_int ~n_det:n_det psi_det
|
||||
end;
|
||||
write_state_average_weight state_average_weight
|
||||
;;
|
||||
|
||||
|
||||
@ -316,11 +356,13 @@ end = struct
|
||||
|> States_number.to_int
|
||||
and ndet =
|
||||
Det_number.to_int b.n_det
|
||||
and ndet_qp_edit =
|
||||
Det_number.to_int b.n_det_qp_edit
|
||||
in
|
||||
let coefs_string i =
|
||||
Array.init nstates (fun j ->
|
||||
let ishift =
|
||||
j*ndet
|
||||
j*ndet_qp_edit
|
||||
in
|
||||
if (ishift < Array.length b.psi_coef) then
|
||||
b.psi_coef.(i+ishift)
|
||||
@ -331,7 +373,7 @@ end = struct
|
||||
)
|
||||
|> Array.to_list |> String.concat "\t"
|
||||
in
|
||||
Array.init ndet (fun i ->
|
||||
Array.init ndet_qp_edit (fun i ->
|
||||
Printf.sprintf " %s\n%s\n"
|
||||
(coefs_string i)
|
||||
(Determinant.to_string ~mo_num:mo_num b.psi_det.(i)
|
||||
@ -472,6 +514,7 @@ psi_det = %s
|
||||
|
||||
(* Handle determinants *)
|
||||
let psi_det =
|
||||
let n_int = N_int_number.of_int @@ (MO_number.get_max () - 1) / 64 + 1 in
|
||||
let n_alpha = Ezfio.get_electrons_elec_alpha_num ()
|
||||
|> Elec_alpha_number.of_int
|
||||
and n_beta = Ezfio.get_electrons_elec_beta_num ()
|
||||
@ -483,8 +526,8 @@ psi_det = %s
|
||||
begin
|
||||
let newdet =
|
||||
(Bitlist.of_string ~zero:'-' ~one:'+' alpha ,
|
||||
Bitlist.of_string ~zero:'-' ~one:'+' beta)
|
||||
|> Determinant.of_bitlist_couple ~alpha:n_alpha ~beta:n_beta
|
||||
Bitlist.of_string ~zero:'-' ~one:'+' beta)
|
||||
|> Determinant.of_bitlist_couple ~n_int ~alpha:n_alpha ~beta:n_beta
|
||||
|> Determinant.sexp_of_t
|
||||
|> Sexplib.Sexp.to_string
|
||||
in
|
||||
@ -492,9 +535,6 @@ psi_det = %s
|
||||
end
|
||||
| _::tail -> read_dets accu tail
|
||||
in
|
||||
let dets =
|
||||
List.map String_ext.rev dets
|
||||
in
|
||||
let a =
|
||||
read_dets [] dets
|
||||
|> String.concat ""
|
||||
@ -510,9 +550,11 @@ psi_det = %s
|
||||
Printf.sprintf "(n_int %d)" (N_int_number.get_max ())
|
||||
and n_states =
|
||||
Printf.sprintf "(n_states %d)" (States_number.to_int @@ read_n_states ())
|
||||
and n_det_qp_edit =
|
||||
Printf.sprintf "(n_det_qp_edit %d)" (Det_number.to_int @@ read_n_det_qp_edit ())
|
||||
in
|
||||
let s =
|
||||
String.concat "" [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det]
|
||||
String.concat "" [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det ; n_det_qp_edit ]
|
||||
in
|
||||
|
||||
|
||||
@ -527,7 +569,9 @@ psi_det = %s
|
||||
Det_number.to_int n_det_new
|
||||
in
|
||||
let det =
|
||||
read ()
|
||||
match read () with
|
||||
| Some x -> x
|
||||
| None -> failwith "No determinants in file"
|
||||
in
|
||||
let n_det_old, n_states =
|
||||
Det_number.to_int det.n_det,
|
||||
@ -558,7 +602,9 @@ psi_det = %s
|
||||
let extract_state istate =
|
||||
Printf.printf "Extracting state %d\n" (States_number.to_int istate);
|
||||
let det =
|
||||
read ()
|
||||
match read () with
|
||||
| Some x -> x
|
||||
| None -> failwith "No determinants in file"
|
||||
in
|
||||
let n_det, n_states =
|
||||
Det_number.to_int det.n_det,
|
||||
@ -588,7 +634,9 @@ psi_det = %s
|
||||
let extract_states range =
|
||||
Printf.printf "Extracting states %s\n" (Range.to_string range);
|
||||
let det =
|
||||
read ()
|
||||
match read () with
|
||||
| Some x -> x
|
||||
| None -> failwith "No determinants in file"
|
||||
in
|
||||
let n_det, n_states =
|
||||
Det_number.to_int det.n_det,
|
||||
@ -614,7 +662,8 @@ psi_det = %s
|
||||
j*n_det
|
||||
in
|
||||
for i=0 to (n_det-1) do
|
||||
det.psi_coef.(!state_shift+i) <- det.psi_coef.(i+ishift)
|
||||
det.psi_coef.(!state_shift+i) <-
|
||||
det.psi_coef.(i+ishift)
|
||||
done
|
||||
end;
|
||||
state_shift := !state_shift + n_det
|
||||
|
||||
@ -65,8 +65,15 @@ end = struct
|
||||
|
||||
|
||||
let read_mo_num () =
|
||||
Ezfio.get_mo_basis_mo_num ()
|
||||
|> MO_number.of_int
|
||||
let elec_alpha_num =
|
||||
Ezfio.get_electrons_elec_alpha_num ()
|
||||
in
|
||||
let result =
|
||||
Ezfio.get_mo_basis_mo_num ()
|
||||
in
|
||||
if result < elec_alpha_num then
|
||||
failwith "More alpha electrons than MOs";
|
||||
MO_number.of_int result
|
||||
|
||||
|
||||
let read_mo_class () =
|
||||
|
||||
@ -43,7 +43,7 @@ $(QP_ROOT)/data/executables: remake_executables element_create_db.byte Qptypes.m
|
||||
$(QP_ROOT)/ocaml/element_create_db.byte
|
||||
|
||||
external_libs:
|
||||
opam install cryptokit core
|
||||
opam install cryptokit sexplib
|
||||
|
||||
qpackage.odocl: $(MLIFILES)
|
||||
ls $(MLIFILES) | sed "s/\.mli//" > qpackage.odocl
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
true: package(cryptokit,zmq,str,sexplib,ppx_sexp_conv,ppx_deriving,getopt)
|
||||
true: package(cryptokit,zarith,zmq,str,sexplib,ppx_sexp_conv,ppx_deriving,getopt)
|
||||
true: thread
|
||||
false: profile
|
||||
<*byte> : linkdep(c_bindings.o), custom
|
||||
|
||||
@ -44,9 +44,12 @@ let psi_det () =
|
||||
let psi_det =
|
||||
Input.Determinants_by_hand.read ()
|
||||
in
|
||||
Input.Determinants_by_hand.to_rst psi_det
|
||||
|> Rst_string.to_string
|
||||
|> print_endline
|
||||
match psi_det with
|
||||
| Some psi_det ->
|
||||
Input.Determinants_by_hand.to_rst psi_det
|
||||
|> Rst_string.to_string
|
||||
|> print_endline
|
||||
| None -> ()
|
||||
|
||||
|
||||
|
||||
|
||||
@ -112,9 +112,9 @@ let set ~core ~inact ~act ~virt ~del =
|
||||
and av = Excitation.create_single act virt
|
||||
in
|
||||
let single_excitations = [ ia ; aa ; av ]
|
||||
|> List.map (fun x ->
|
||||
|> List.map (fun z ->
|
||||
let open Excitation in
|
||||
match x with
|
||||
match z with
|
||||
| Single (x,y) ->
|
||||
( MO_class.to_bitlist n_int (Hole.to_mo_class x),
|
||||
MO_class.to_bitlist n_int (Particle.to_mo_class y) )
|
||||
@ -187,9 +187,10 @@ let set ~core ~inact ~act ~virt ~del =
|
||||
match aa with
|
||||
| Double _ -> assert false
|
||||
| Single (x,y) ->
|
||||
( MO_class.to_bitlist n_int (Hole.to_mo_class x) ) @
|
||||
( MO_class.to_bitlist n_int (Particle.to_mo_class y) )
|
||||
|> Bitlist.to_int64_list
|
||||
Bitlist.to_int64_list
|
||||
( MO_class.to_bitlist n_int ( Hole.to_mo_class x) ) @
|
||||
Bitlist.to_int64_list
|
||||
( MO_class.to_bitlist n_int (Particle.to_mo_class y) )
|
||||
in
|
||||
Ezfio.set_bitmasks_n_mask_cas 1;
|
||||
Ezfio.ezfio_array_of_list ~rank:3 ~dim:([| (N_int_number.to_int n_int) ; 2; 1|]) ~data:result
|
||||
|
||||
470
ocaml/qp_tunnel.ml
Normal file
470
ocaml/qp_tunnel.ml
Normal file
@ -0,0 +1,470 @@
|
||||
open Qputils
|
||||
open Qptypes
|
||||
|
||||
type ezfio_or_address = EZFIO of string | ADDRESS of string
|
||||
type req_or_sub = REQ | SUB
|
||||
|
||||
let localport = 42379
|
||||
|
||||
|
||||
let in_time_sum = ref 1.e-9
|
||||
and in_size_sum = ref 0.
|
||||
|
||||
|
||||
let () =
|
||||
let open Command_line in
|
||||
begin
|
||||
"Creates an ssh tunnel for using slaves on another network. Launch a server on the front-end node of the cluster on which the master process runs. Then start a client ont the front-end node of the distant cluster."
|
||||
|
||||
|> set_footer_doc ;
|
||||
|
||||
[ { short='g' ; long="get-input" ; opt=Optional ;
|
||||
doc="Downloads the EZFIO directory." ;
|
||||
arg=Without_arg; } ;
|
||||
|
||||
{ short='v' ; long="verbose" ; opt=Optional ;
|
||||
doc="Prints the transfer speed." ;
|
||||
arg=Without_arg; } ;
|
||||
|
||||
anonymous
|
||||
"(EZFIO_DIR|ADDRESS)"
|
||||
Mandatory
|
||||
"EZFIO directory or address.";
|
||||
] |> set_specs
|
||||
end;
|
||||
|
||||
let arg =
|
||||
let x =
|
||||
match Command_line.anon_args () with
|
||||
| [x] -> x
|
||||
| _ -> begin
|
||||
Command_line.help () ;
|
||||
failwith "EZFIO_FILE or ADDRESS is missing"
|
||||
end
|
||||
in
|
||||
if Sys.file_exists x && Sys.is_directory x then
|
||||
EZFIO x
|
||||
else
|
||||
ADDRESS x
|
||||
in
|
||||
|
||||
let verbose =
|
||||
Command_line.get_bool "verbose"
|
||||
in
|
||||
|
||||
|
||||
|
||||
let localhost =
|
||||
Lazy.force TaskServer.ip_address
|
||||
in
|
||||
|
||||
|
||||
let long_address =
|
||||
match arg with
|
||||
| ADDRESS x -> x
|
||||
| EZFIO x ->
|
||||
let ic =
|
||||
Filename.concat (Qpackage.ezfio_work x) "qp_run_address"
|
||||
|> open_in
|
||||
in
|
||||
let result =
|
||||
input_line ic
|
||||
|> String.trim
|
||||
in
|
||||
close_in ic;
|
||||
result
|
||||
in
|
||||
|
||||
let protocol, address, port =
|
||||
match String.split_on_char ':' long_address with
|
||||
| t :: a :: p :: [] -> t, a, int_of_string p
|
||||
| _ -> failwith @@
|
||||
Printf.sprintf "%s : Malformed address" long_address
|
||||
in
|
||||
|
||||
|
||||
let zmq_context =
|
||||
Zmq.Context.create ()
|
||||
in
|
||||
|
||||
|
||||
(** Check availability of the ports *)
|
||||
let localport =
|
||||
let dummy_socket =
|
||||
Zmq.Socket.create zmq_context Zmq.Socket.rep
|
||||
in
|
||||
let rec try_new_port port_number =
|
||||
try
|
||||
List.iter (fun i ->
|
||||
let address =
|
||||
Printf.sprintf "tcp://%s:%d" localhost (port_number+i)
|
||||
in
|
||||
Zmq.Socket.bind dummy_socket address;
|
||||
Zmq.Socket.unbind dummy_socket address
|
||||
) [ 0;1;2;3;4;5;6;7;8;9 ] ;
|
||||
port_number
|
||||
with
|
||||
| Unix.Unix_error _ -> try_new_port (port_number+100)
|
||||
in
|
||||
let result =
|
||||
try_new_port localport
|
||||
in
|
||||
Zmq.Socket.close dummy_socket;
|
||||
result
|
||||
in
|
||||
|
||||
|
||||
let create_socket sock_type bind_or_connect addr =
|
||||
let socket =
|
||||
Zmq.Socket.create zmq_context sock_type
|
||||
in
|
||||
let () =
|
||||
try
|
||||
bind_or_connect socket addr
|
||||
with
|
||||
| _ -> failwith @@
|
||||
Printf.sprintf "Unable to establish connection to %s." addr
|
||||
in
|
||||
socket
|
||||
in
|
||||
|
||||
|
||||
(* Handle termination *)
|
||||
let run_status = ref true in
|
||||
let handler =
|
||||
Sys.Signal_handle (fun signum ->
|
||||
run_status := false;
|
||||
Sys.set_signal signum Sys.Signal_default
|
||||
)
|
||||
in
|
||||
Sys.set_signal Sys.sigusr1 handler;
|
||||
Sys.set_signal Sys.sigint handler;
|
||||
|
||||
|
||||
let new_thread req_or_sub addr_in addr_out =
|
||||
let socket_in, socket_out =
|
||||
match req_or_sub with
|
||||
| REQ ->
|
||||
create_socket Zmq.Socket.router Zmq.Socket.bind addr_in,
|
||||
create_socket Zmq.Socket.dealer Zmq.Socket.connect addr_out
|
||||
| SUB ->
|
||||
create_socket Zmq.Socket.sub Zmq.Socket.connect addr_in,
|
||||
create_socket Zmq.Socket.pub Zmq.Socket.bind addr_out
|
||||
in
|
||||
|
||||
if req_or_sub = SUB then
|
||||
Zmq.Socket.subscribe socket_in "";
|
||||
|
||||
|
||||
(*
|
||||
let action =
|
||||
if verbose then
|
||||
begin
|
||||
match req_or_sub with
|
||||
| REQ -> (fun () ->
|
||||
let msg =
|
||||
Zmq.Socket.recv_all socket_in
|
||||
in
|
||||
let t0 = Unix.gettimeofday () in
|
||||
Zmq.Socket.send_all socket_out msg;
|
||||
let in_size =
|
||||
float_of_int ( List.fold_left (fun accu x -> accu + String.length x) 0 msg )
|
||||
/. 8192. /. 1024.
|
||||
in
|
||||
let msg =
|
||||
Zmq.Socket.recv_all socket_out
|
||||
in
|
||||
let t1 = Unix.gettimeofday () in
|
||||
Zmq.Socket.send_all socket_in msg;
|
||||
let in_time = t1 -. t0 in
|
||||
in_time_sum := !in_time_sum +. in_time;
|
||||
in_size_sum := !in_size_sum +. in_size;
|
||||
Printf.printf " %16.2f MiB/s -- %16.2f MiB/s\n%!" (in_size /. in_time) (!in_size_sum /. !in_time_sum);
|
||||
)
|
||||
| SUB -> (fun () ->
|
||||
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
|
||||
end
|
||||
else
|
||||
begin
|
||||
match req_or_sub with
|
||||
| REQ -> (fun () ->
|
||||
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out;
|
||||
Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in )
|
||||
| SUB -> (fun () ->
|
||||
Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
|
||||
end
|
||||
in
|
||||
*)
|
||||
|
||||
let action_in =
|
||||
match req_or_sub with
|
||||
| REQ -> (fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
|
||||
| SUB -> (fun () -> Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
|
||||
in
|
||||
|
||||
let action_out =
|
||||
match req_or_sub with
|
||||
| REQ -> (fun () -> Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in )
|
||||
| SUB -> (fun () -> () )
|
||||
in
|
||||
|
||||
let pollitem =
|
||||
Zmq.Poll.mask_of
|
||||
[| (socket_in, Zmq.Poll.In) ; (socket_out, Zmq.Poll.In) |]
|
||||
in
|
||||
|
||||
|
||||
while !run_status do
|
||||
|
||||
let polling =
|
||||
Zmq.Poll.poll ~timeout:1000 pollitem
|
||||
in
|
||||
|
||||
match polling with
|
||||
| [| Some Zmq.Poll.In ; Some Zmq.Poll.In |] -> ( action_out () ; action_in () )
|
||||
| [| _ ; Some Zmq.Poll.In |] -> action_out ()
|
||||
| [| Some Zmq.Poll.In ; _ |] -> action_in ()
|
||||
| _ -> ()
|
||||
done;
|
||||
|
||||
Zmq.Socket.close socket_in;
|
||||
Zmq.Socket.close socket_out;
|
||||
in
|
||||
|
||||
|
||||
|
||||
let ocaml_thread =
|
||||
let addr_out =
|
||||
Printf.sprintf "tcp:%s:%d" address port
|
||||