Installing xcrysden

hanamilani · 02-12-2013, 11:58 AM

Hello,

I have downloaded the source file of xcrysden and I have un-tar it. I do not understand this part of the installation manual:

"each user should define two environmental variables: XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH. This can be facilitated by the xcConfigure script which in addition asks some questions and configures the package accoring to user's wishes. From XCrySDen root directory execute:

./xcConfigure"

How should I define XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH ?

Thanks for your help.

John VV · 02-12-2013, 10:52 PM

first off just what did you download ?
http://www.xcrysden.org/Download.html#__toc__1
the source code ?
xcrysden-1.5.53.tar.gz

or the prebuilt shared
xcrysden-1.5.53-linux_x86_64-shared.tar.gz

i had to search you to find out you are using OpenSUSE12.1 ( it hits it's End of Life in 91 days )
-- time to think of installing OpenSUSE 12.2

the instructions will be very different depending on just what you downloaded

Quote:

How should I define XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH ?

well seeing as SUSE dose things very differently than every other RPM based distro , most "average" instructions do not work

-- life with SUSE

INSTALL the prerequisites !!!
tk/tcl
mesa ( the nvidia.run provides some of this but changes mesa so it you have a nvidia card and use the .run reinstall mesa )

Code:

su -
zypper in tk tk-devel tcl tcl-devel Mesa Mesa-devel

for the prebuilt

you set the variable
from the install instructions
http://www.xcrysden.org/doc/install.html

run the script
"./xcConfigure"

or manually
i am using "/usr/opt/xcrysden" in this example

make the folder " scratch "

Code:

su -
makdir /usr/opt/xcrysden/scratch

1) for a single user
edit ~/.profile -- see text below
then log out and back in

2) system wide
make a new text file called "/etc/profile.local"

-- then reboot !!! -- see text below

add this text
EDITED FOR YOUR SETUP and install location
i am using /usr/opt/xcrysden

Code:

XCRYSDEN_TOPDIR=/usr/opt/xcrysden
XCRYSDEN_SCRATCH=/usr/opt/xcrysden/scratch

export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH

hanamilani · 02-13-2013, 08:54 AM

Thanks for your detailed response and thank you for searching me to find to see what linux I am using. "Today" I am using Fedora 18, the reason I shifted to Fedora was the constant failure of opensuse while I was running my codes and the time to time hanging of my laptop !!! (I hope it is not an offence to anyone, but that's what happened to me)

Getting back to xcrysden: I have downloaded the source code. I followed the steps like this:

1. tar -zxvf xcrysden-1.5.53.tar.gz
2. cd xcrysden-1.5.53
3. su
4. XCRYSDEN_TOPDIR=/usr/local/xcrysden
5. XCRYSDEN_SCRATCH=/usr/local/xcrysden_scratch
6. mkdir /usr/local/xcrysden_scratch
7. cd scripts
8. ./xcConfigure
9. answering the questions ....
10. source ~/.bashrc
11. xcrysden

and here is the result:

Quote:

+-----------------------------------------------------------------+
|*****************************************************************|
|* *|
|* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*---------------------------------------------------------------*|
|* *|
|* Anton Kokalj (tone.kokalj@ijs.si) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2012 by Anton Kokalj *|
|* *|
|*****************************************************************|
+-----------------------------------------------------------------+

Version: 1.5.53

Please report bugs to: tone.kokalj@ijs.si

TERMS OF USE:
-------------
XCRYSDEN is released under the GNU General Public License.

Whenever graphics generated by XCRYSDEN are used in scientific
publications, it shall be greatly appreciated to include an explicit
reference. The preferred form is the following:

[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/sara/CODES/xcrysden-1.5.53
XCRYSDEN_SCRATCH=/usr/local/xcrysden_scratch

/home/sara/CODES/xcrysden-1.5.53/xcrysden: line 230: /home/sara/CODES/xcrysden-1.5.53/bin/xcrys: No such file or directory

There is something wrong with defining the scratch and top directories, but I don't know what it really is. I would be grateful if you help me.

knudfl · 02-13-2013, 11:42 AM

#3 : Fedora 18 and xcrysden-1.5.53 : No issues.
( The 32bits (i686) Fedora 18 was used for the test build.)

Your issues : May be you are using an old "Instruction" ?
Please see the file README : 3.2 COMPILATION:, line 123.

Prerequisites :
# yum install gcc-c++ gcc-gfortran fftw-devel tcl-devel tk-devel \
mesa-libGLU-devel mesa-libGL-devel wget

Suggest : Unpack xcrysden-1.5.53.tar.gz in /home/sara/ :
tar xvf xcrysden-1.5.53.tar.gz && cd xcrysden-1.5.53/
cp system/Make.sys-shared Make.sys
make all
.. And after a successful make the command $ ./xcrysden
.. will open the "Xcrysden GUI"

No extra settings are required, but are automatically set to:
XCRYSDEN_TOPDIR=/home/<name>/xcrysden-1.5.53
XCRYSDEN_SCRATCH=/tmp

( Settings may be required if you choose to do # make install ).

-

hanamilani · 02-13-2013, 12:46 PM

Thanks for your post. I took all your suggestions and this is the results I got:

Quote:

TERMS OF USE:
-------------
XCRYSDEN is released under the GNU General Public License.

Whenever graphics generated by XCRYSDEN are used in scientific
publications, it shall be greatly appreciated to include an explicit
reference. The preferred form is the following:

[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.

./xcrysden: line 163: /home/sara/CODES/xcrysden-1.5.53-bin-shared/scripts/xcLib.sh: No such file or directory

hanamilani · 02-13-2013, 01:03 PM

This is strange, I am seeing xcLib.sh in /home/sara/CODES/xcrysden-1.5.53/scripts
Why does it want to read this file from /home/sara/CODES/xcrysden-1.5.53-bin-shared ?!?!?!

knudfl · 02-13-2013, 01:28 PM

#5, #6 : Don't know.
This is the text in the terminal, when xcrysden has started :

Code:

$ ./xcrysden 

+-----------------------------------------------------------------+
|*****************************************************************|
|*                                                               *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*               =         ===         =              ===        *|
|*---------------------------------------------------------------*|
|*                                                               *|                                                                                          
|*    Anton Kokalj (tone.kokalj@ijs.si)                          *|                                                                                          
|*    Jozef Stefan Institute, Ljubljana, Slovenia                *|                                                                                          
|*                                                               *|                                                                                          
|*    Copyright (c) 1996--2012 by Anton Kokalj                   *|                                                                                          
|*                                                               *|                                                                                          
|*****************************************************************|                                                                                          
+-----------------------------------------------------------------+                                                                                          
                                                                                                                                                             
  Version: 1.5.53                                                                                                                                            
                                                                                                                                                             
  Please report bugs to: tone.kokalj@ijs.si                                                                                                                  
                                                                                                                                                             
                                                                                                                                                             
  TERMS OF USE:                                                                                                                                              
  -------------                                                                                                                                              
  XCRYSDEN is released under the GNU General Public License.                                                                                                 
                                                                                                                                                             
  Whenever graphics generated by XCRYSDEN are used in scientific                                                                                             
  publications, it shall be greatly appreciated to include an explicit                                                                                       
  reference. The preferred form is the following:                                                                                                            
                                                                                                                                                             
  [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.                                                                                                 
        Code available from http://www.xcrysden.org/.                                                                                                        
                                                                                                                                                             
XCRYSDEN_TOPDIR=/home/knudfl/xcrysden-1.5.53
XCRYSDEN_SCRATCH=/tmp

Running on platform : unix
   Operating system : Linux
Executing: /home/knudfl/xcrysden-1.5.53/bin/ftnunit

John VV · 02-13-2013, 01:32 PM

switch from opsesuse 12 to fedora 18
odd opensuse is normally much more stable than fedora , from my experience.

i do not have a fedora install so ...
fallow knudfl instructions for the source build
( his 32 bit build looks like it works with fedora18's gcc 4.7.2 and gcc-fortran 4.7 )
--- i would have thought there would be issues , but i would have been wrong ---

Quote:

/home/sara/CODES/xcrysden-1.5.53-bin-shared/scripts/xcLib.sh: No such file or directory

this looks like the "XCRYSDEN_TOPDIR" is not set 100% correct
double check it

"xcrysden-1.5.53-bin-shared" dose not match "XCRYSDEN_TOPDIR=/home/sara/CODES/xcrysden-1.5.53"
do you have a folder in the SAME folder as xcrysden-1.5.53
/home/sara/CODES/xcrysden-1.5.53
/home/sara/CODES/xcrysden-1.5.53-bin-shared
or is "xcrysden-1.5.53-bin-shared"
in the "xcrysden-1.5.53" folder

--- edited later ---

i just did the source build on opensuse 12.2 64 bit
using ONLY "knudfl instructions"
from the "xcrysden-1.5.53/" folder

Code:

cp system/Make.sys-shared Make.sys
make all
./xcrysden

i am guessing you ALSO set the variables for the "pre-built" version

unset then from ~/.bashrc or ( for fedora ) /etc/profile
depending on what you used to set them

then in the "xcrysden-1.5.53/" folder
run

Code:

make clean 
make all
./xcrysden

knudfl · 02-13-2013, 01:56 PM

# 6 : Which Fedora 18 have you got ? i686 or x86_64 ?
This command will tell : $ uname -m

# 8 : Seems like there is a bug? in a file.c, which is no problem for gcc-4.7.2.
... Or could be the combination of the all the libraries used at compile time,
that just works on Fedora 18. ( Xcrysden fails here too on some "other OS".)

-

John VV · 02-13-2013, 02:06 PM

it builds and runs on opensuse 12.2 ( gcc 4.7.1 & gfortran4.7 )

i am guessing it is a mix of fallowing the prebuilt instructions for the source build

one thing hanamilani there is a README in the source folder
using the provided README for a source build is almost always better than instructions on the web

normally there is a README ( and / or) INSTALL file ,or a folder called "Doc" in most source code packages

use those instructions first before any on the web

hanamilani · 02-14-2013, 03:16 AM

John VV, knudfl

Thanks for the time you put on my question.
For those who may encounter the same trouble, I leave the comments that solved my problem as follows:

Quote:

$ tar xvf xcrysden-1.5.53.tar.gz
$ cd xcrysden-1.5.53/
$ cp system/Make.sys-shared Make.sys
$ make all
$ unset XCRYSDEN_TOPDIR
$ ./xcrysden

Regarding the shift to fedora, I don't know if it is ok to put it here or not but I would be grateful if both of you let me know your opinion:
I am working on DELL E6510 and I have now installed fedora 18 x86_64 and I usually run codes in parallel using gfortran and mpich2. I am a fan of opensuse, since it was the first linux that helped me get used to linux OS. (I am not an expert but an on/off user) I had opensuse 11.0 for a long time and never encountered a failure or hanging problem even when I was using the full capacity of my processors).
But, since I shifted to opensuse 12.00 and higher, I had problems. Even if the system was left out idle after a few minutes, it was like fire burning out of it !!! Or when I wanted to run my code in parallel with 4 cpus, it started shouting !!! Another case was when I was working with mono it hanged all the time.

People would tell me that it is the problem of my graphic card. But it remained a mystery for me until I shifted to fedora. Now, my laptop works fine and runs day and night with no extra heat, no shout, no hang !!! But still I am interested to know where I was going wrong with opensuse.

Thanks again...