Added INSTALL.md

INSTALL.md

@@ -0,0 +1,64 @@
+# Installation
+
+## Requirements
+
+* curl
+* wget
+* m4
+* GNU make
+* Intel Fortran compiler
+* Python
+* Bash
+
+
+By default, the Ocaml compiler will be installed in `$HOME/ocamlbrew`.
+To install it somewhere else, set the `$OCAMLBREW_BASE` environment
+variable to the required destination, for example:
+
+    export OCAMLBREW_BASE=/usr/local/ocamlbrew
+
+For more info about the Ocaml installation, check the ocamlbrew
+website : https://github.com/hcarty/ocamlbrew
+
+
+
+## Installing behind a firewall
+
+1) Download `tsocks`:
+
+    wget http://sourceforge.net/projects/tsocks/files/latest/download
+    mv download tsocks.tar.gz
+
+2) Tranfer `tsocks.tar.gz` on the remote host
+
+3) Configure `tsocks` with the proper directory for the `tsocks.conf` file:
+
+    tar -zxvf tsocks.tar.gz
+    cd tsocks-*
+    ./configure --with-conf=${PWD}/tsocks.conf
+
+4) Create the `tsocks.conf` file with the following content:
+
+    server = 127.0.0.1
+    server_port = 10000
+
+5) Create the tsocks library:
+
+    make
+
+6) Add the `libtsocks.so` to the `LD_PRELOAD` environment variable:
+
+    export LD_PRELOAD="${PWD}/libtsocks.so.1.8"
+
+7) Create a custom curl command to set the tsocks option: open a file named
+   `curl`, which is accessible from your `PATH` environment variable before the
+   real `curl` command, and fill this file with:
+
+    #!/bin/bash
+    /usr/bin/curl --socks5 127.0.0.1:10000 $@
+
+8) Start a tsocks ssh tunnel:
+
+    ssh -fN -D 10000 user@external-server.com
+
+

README.md

@@ -5,4 +5,4 @@ Quantum package
 
 Set of quantum chemistry programs and libraries.
 
-For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>)
+For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>), or the [Install](Install.md) file.

ocaml/qp_run.ml

@@ -32,9 +32,6 @@ let run exe ezfio_file =
   if (Sys.file_exists_exn fifo_name) then
     Sys.remove fifo_name;
   Unix.mkfifo ~perm:0o664 fifo_name;
-  let script = Printf.sprintf "%s/scripts/follow_output.py %s &
-  echo $! > %s &" Qpackage.root ezfio_file fifo_name in
-  ignore (Sys.command script);
 
   let pid = 
     In_channel.with_file fifo_name ~f:(fun in_channel ->

src/Makefile

@@ -19,7 +19,7 @@ $(NEEDED_MODULES): FORCE
 
 executables:
 	rm -f executables ; \
-	for EXE in $$(find $(QPACKAGE_ROOT)/src -type f -executable | grep -e "$(QPACKAGE_ROOT)/src/[^/]*/[^/]*$$" ) ; \
+	for EXE in $$(find $(QPACKAGE_ROOT)/src -perm /u+x -type f | grep -e "$(QPACKAGE_ROOT)/src/[^/]*/[^/]*$$" |sort ) ; \
 	  do printf "%-30s %s\n" $$(basename $$EXE) $$EXE | sed "s|$(QPACKAGE_ROOT)|\$$QPACKAGE_ROOT|g" >> executables ;\
 	done
 

src/Output/output.irp.f

@@ -24,12 +24,12 @@ BEGIN_SHELL [ /bin/bash ]
   call ezfio_set_output_empty(.False.)
 IRP_IF COARRAY
   if (this_image() == 1) then
-    output_$NAME = getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a')
+    output_$NAME = 6 !getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a')
   else
     output_$NAME = getUnitAndOpen('/dev/null','w')
   endif
 IRP_ELSE
-  output_$NAME = getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a')
+  output_$NAME = 6 !getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a')
 IRP_ENDIF
   write(output_$NAME,'(A)')                                          &
       '--------------------------------------------------------------------------------'

src/Utils/progress.irp.f

@@ -12,7 +12,7 @@ subroutine start_progress(max,title,progress_init)
   progress_title = title
   progress_active = .True.
   progress_value = progress_init
-  call run_progress()
+! call run_progress()
 
 end