635. Installing R on Rocks 5.4.3

Rocks 5.4.3 is based on CentOS 5.6 which is practically ancient by now (released Jan 2011).

Either way, when dealing with someone else's cluster its better to not fiddle too much with what is already working.

Here's a not at all elegant way of install R on Rocks 5.4.3

wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/R-core-3.3.2-3.el5.x86_64.rpm
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/R-3.3.2-3.el5.x86_64.rpm 
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/R-devel-3.3.2-3.el5.x86_64.rpm 
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/libRmath-3.3.2-3.el5.x86_64.rpm 
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/libRmath-devel-3.3.2-3.el5.x86_64.rpm 
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/R-core-devel-3.3.2-3.el5.x86_64.rpm
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/libssh2-0.18-10.el5.x86_64.rpm 
wget http://mirror.nsw.coloau.com.au/epel/5/x86_64/xdg-utils-1.0.2-4.el5.noarch.rpm 
wget http://mirror.centos.org/centos/5/os/x86_64/CentOS/xz-devel-4.999.9-0.3.beta.20091007git.el5.x86_64.rpm
wget http://mirror.centos.org/centos/5/os/x86_64/CentOS/texinfo-tex-4.8-14.el5.x86_64.rpm
wget http://mirror.centos.org/centos/5/os/x86_64/CentOS/texinfo-4.8-14.el5.x86_64.rpm

sudo yum install R-3.3.2-3.el5.x86_64.rpm libRmath-devel-3.3.2-3.el5.x86_64.rpm libRmath-3.3.2-3.el5.x86_64.rpm R-devel-3.3.2-3.el5.x86_64.rpm R-core-3.3.2-3.el5.x86_64.rpm R-core-devel-3.3.2-3.el5.x86_64.rpm libssh2-0.18-10.el5.x86_64.rpm xdg-utils-1.0.2-4.el5.noarch.rpm texinfo-tex-4.8-14.el5.x86_64.rpm xz-devel-4.999.9-0.3.beta.20091007git.el5.x86_64.rpm texinfo-4.8-14.el5.x86_64.rpm 

[..]
Total size: 169 M
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing     : libssh2                                                                                                                                                                                                               1/11 
  Installing     : libRmath                                                                                                                                                                                                              2/11 
  Installing     : texinfo                                                                                                                                                                                                               3/11 
  Installing     : texinfo-tex                                                                                                                                                                                                           4/11 
  Installing     : libRmath-devel                                                                                                                                                                                                        5/11 
  Installing     : xz-devel                                                                                                                                                                                                              6/11 
  Installing     : xdg-utils                                                                                                                                                                                                             7/11 
  Installing     : R-core                                                                                                                                                                                                                8/11 
  Installing     : R-core-devel                                                                                                                                                                                                          9/11 
  Installing     : R-devel                                                                                                                                                                                                              10/11 
  Installing     : R                                                                                                                                                                                                                    11/11 

Installed:
  R.x86_64 0:3.3.2-3.el5           R-core.x86_64 0:3.3.2-3.el5     R-core-devel.x86_64 0:3.3.2-3.el5     R-devel.x86_64 0:3.3.2-3.el5       libRmath.x86_64 0:3.3.2-3.el5                          libRmath-devel.x86_64 0:3.3.2-3.el5    
  libssh2.x86_64 0:0.18-10.el5     texinfo.x86_64 0:4.8-14.el5     texinfo-tex.x86_64 0:4.8-14.el5       xdg-utils.noarch 0:1.0.2-4.el5     xz-devel.x86_64 0:4.999.9-0.3.beta.20091007git.el5    

Complete!

Testing:

R

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> q()
Save workspace image? [y/n/c]: n

634. Compiling EQ3/6 on Debian

EQ3/6, a program for calculation of geochemical equilibrium in aqueous systems and which can be downloaded here, has a spectacularly unhelpful Install.txt file.

Sadly, we do not provide specific instructions on how to compile and link
the software to build the executables. You have to figure that out yourself
for your specific platform. It will require some number of steps. Also, we 
do not provide makefiles. It is not necessary to use make files, although
some people like them. If all this seems to exceed your knowledge and capacity,
seek the assistance of a qualified Linux or Unix maven who knows how to do
these things on your platform. 

---

Here I describe how I went about to compile it.

---

1. Download EQ36_80a_linux.zip from https://www-gs.llnl.gov/about/energy-security/geochemistry

---

2. Extract it. Move the EQ3_6v8.0a folder to ~
You can put it wherever you want, but then need to edit eq36cfg, and you'll have to deal with csh not handling long paths that well. It's just easier to give up and put EQ3_6v8.0a under $HOME

---

3. Time to extract further, compile and set up

cd ~/EQ3_6v8.0a
ls *.tar |xargs -I {} tar xvf {}
find -name "*.gz"|xargs -I {} gunzip {}

Time to look at what we have. There are .f files in

xcon6/src
eq3nr/src
eqlib/src
eqlibu/src
eq6/src
xcon3/src
eqpt/src
eqlibg/src

A lot of these are subroutines. We'll compile all files as modules and make static libraries

cd eqlibg/src
gfortran -c *.f
ar cr eqlibg.a *.o
cd ../../eqlibu/src
gfortran -c *.f
ar cr eqlibu.a *.o
cd ../../eqlib/src
gfortran -c *.f
ar cr eqlib.a *.o

cd ../../eqpt/src
sh makelinks
gfortran *.f *.a -o eqpt
cp eqpt ../../bin/
cd ../../xcon3/src
sh makelinks
gfortran *.f *.a -o xcon3
cp xcon3 ../../bin/
cd ../../xcon6/src
sh makelinks
gfortran *.f *.a -o xcon6
cp xcon6 ../../bin/
cd ../../eq3nr/src
sh makelinks
gfortran *.f *.a -o eq3nr
cp eq3nr ../../bin/
cd ../../eq6/src
sh makelinks
gfortran *.f *.a -o eq6

You'll get

eq6.f:16.9:

      use mod6pt                                                        
         1
Fatal Error: Can't open module file 'mod6pt.mod' for reading at (1): No such file or directory
eqcalc.f:77.9:

      use mod6pt                                                        
         1
Fatal Error: Can't open module file 'mod6pt.mod' for reading at (1): No such file or directory
eqphas.f:129.9:

      use mod6pt                                                        
         1
Fatal Error: Can't open module file 'mod6pt.mod' for reading at (1): No such file or directory
eqshel.f:146.9:

      use mod6pt                                                        
         1
Fatal Error: Can't open module file 'mod6pt.mod' for reading at (1): No such file or directory
exivar.f:121.9:

      use mod6pt                                                        
         1
Fatal Error: Can't open module file 'mod6pt.mod' for reading at (1): No such file or directory

Don't despair, just run again:

gfortran *.f *.a -o eq6
cp eq6 ../../bin/

You should now have a bin/ that looks like

eq3nr  eq6  eqpt  readme.txt  runeq3  runeq6  runeqpt  xcif3  xcif6  xcon3  xcon6

cd ~/EQ3_6v8.0a
cat eq36cfg >> ~/.cshrc
cd scripts/
ln -s runeq36 runeq3
ln -s runeq36 runeq6
sudo mkdir /usr/tmp
sudo chmod ugo+rw /usr/tmp
cd ../db/
csh ../scripts/runeqpt all

------------------------------------
All done

---

4. Test

cd ~/EQ3_6v8.0a/3tlib_fmt
csh ../scripts/runeq36 fmt ../db/data0 c4pgwbN2.3i

[..]
Done. Optimization ended outside requested limits.


 Starting hybrid Newton-Raphson iteration.

   Done. Hybrid Newton-Raphson iteration converged in  56 iterations.


 * Warning - (EQ3NR/eq3nr) The calculated TDS of 3.44395E+05 mg/L
       differs from the input file value of 3.54016E+05 mg/L
       by more than 1%. The calculated value will be used in
       subsequent calculations.

 The pickup file has been written.

 No further input found.


          Start time = 13:57:15  21Mar2017
            End time = 13:57:15  21Mar2017

           Run time =  0.586E-01 seconds

 Normal exit
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG
------------------------------------

  The following output files were written:

    c4pgwbN2.3o
    c4pgwbN2.3p

------------------------------------

  The following input files were run without generating
  any EQ3NR error messages:

    c4pgwbN2.3i

------------------------------------
All done

The question here is whether the error is indicative of a serious issue with the compiled software.

I reran as

csh ../scripts/runeq3 fmt c4pgwbN2.3i |tee c4pgwbN2.3o

and compared

diff c4pgwbN2.3o Outputs/c4pgwbN2.3o

18c18
<  Run  14:12:44  21Mar2017
---
>  Run  13:18:06  07Sep2011
870,871c870,871
<              -0.0000 per cent of the total charge
<              -0.0000 per cent of the mean charge
---
>               0.0000 per cent of the total charge
>               0.0000 per cent of the mean charge
1235,1236c1235,1236
<           Start time = 14:12:44  21Mar2017
<             End time = 14:12:44  21Mar2017
---
>           Start time = 13:18:06  07Sep2011
>             End time = 13:18:06  07Sep2011
1238c1238
<            Run time =  0.586E-01 seconds
---
>            Run time =  0.781E-01 seconds

The results are the same.We're good.

---

Everything put together as a script:

mkdir ~/tmp
cd ~/tmp
wget http://www-gs.llnl.gov/content/assets/docs/energy/EQ36_80a_Linux.zip
unzip EQ36_80a_Linux.zip
cd Linux
mv EQ3_6v8.0a ~/
rm -rf Linux
cd ~/EQ3_6v8.0a
ls *.tar |xargs -I {} tar xvf {}
find -name "*.gz"|xargs -I {} gunzip {}
cd eqlibg/src
gfortran -c *.f
ar cr eqlibg.a *.o
cd ../../eqlibu/src
gfortran -c *.f
ar cr eqlibu.a *.o
cd ../../eqlib/src
gfortran -c *.f
ar cr eqlib.a *.o

cd ../../eqpt/src
sh makelinks
gfortran *.f *.a -o eqpt
cp eqpt ../../bin/
cd ../../xcon3/src
sh makelinks
gfortran *.f *.a -o xcon3
cp xcon3 ../../bin/
cd ../../xcon6/src
sh makelinks
gfortran *.f *.a -o xcon6
cp xcon6 ../../bin/
cd ../../eq3nr/src
sh makelinks
gfortran *.f *.a -o eq3nr
cp eq3nr ../../bin/
cd ../../eq6/src
sh makelinks
gfortran *.f *.a -o eq6
gfortran *.f *.a -o eq6
cp eq6 ../../bin/

cd ~/EQ3_6v8.0a

cat eq36cfg >> ~/.cshrc

cd scripts/
ln -s runeq36 runeq3
ln -s runeq36 runeq6

sudo mkdir /usr/tmp
sudo chmod ugo+rw /usr/tmp

cd ../db/
csh ../scripts/runeqpt all

633. Multiwfn on debian, with gaussian

Not much to say. I wanted to do some Bader-type AIM analyses, and I don't have AIM2000/AIMPAC. Multiwfn can do this, and a lot more.

---

Setting up multiwfn
Download the precompiled Multiwfn binaries here: https://multiwfn.codeplex.com/

Extract the binary and the copy the directory to .e.g /opt

$ ls /opt/Multiwfn_3.3.9_bin_Linux/
examples  Multiwfn  settings.ini

Edit your ~/.bashrc and add:

export KMP_STACKSIZE=64000000
export Multiwfnpath=/opt/Multiwfn_3.3.9_bin_Linux

When I hit 0 to visualize something, the plot screen is empty. Check/uncheck a box in the window and the plot will show.

---

Generating wfx files in gaussian:
If you've already run a job that has generated a .chk file, then run a simple quick job like this:

%nprocshared=2
%mem=500Mb
%chk=test.chk
#P chkbasis geom=allcheck guess=(check,only) output=wfx pop=(none)

test.wfx

---

To analyse the .wfx file using multiwfn, look at the examples in the manual: https://www.codeplex.com/Download?ProjectName=multiwfn&DownloadId=1607667
The strength of multiwfn is that it can do a LOT. That's also its weakness, in the sense that the menu options are a bit overwhelming. Following the examples in the manual is probably mandatory.