LinuxQuestions.org
Visit the LQ Articles and Editorials section
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Software
User Name
Password
Linux - Software This forum is for Software issues.
Having a problem installing a new program? Want to know which application is best for the job? Post your question in this forum.

Notices

Reply
 
Search this Thread
Old 02-12-2013, 11:58 AM   #1
hanamilani
Member
 
Registered: Dec 2008
Posts: 66

Rep: Reputation: 0
Installing xcrysden


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.
 
Old 02-12-2013, 10:52 PM   #2
John VV
Guru
 
Registered: Aug 2005
Posts: 13,082

Rep: Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747
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

Last edited by John VV; 02-12-2013 at 10:58 PM.
 
Old 02-13-2013, 08:54 AM   #3
hanamilani
Member
 
Registered: Dec 2008
Posts: 66

Original Poster
Rep: Reputation: 0
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.
 
Old 02-13-2013, 11:42 AM   #4
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014.08, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,981

Rep: Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610
#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 ).

-

Last edited by knudfl; 02-13-2013 at 11:45 AM.
 
Old 02-13-2013, 12:46 PM   #5
hanamilani
Member
 
Registered: Dec 2008
Posts: 66

Original Poster
Rep: Reputation: 0
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
 
Old 02-13-2013, 01:03 PM   #6
hanamilani
Member
 
Registered: Dec 2008
Posts: 66

Original Poster
Rep: Reputation: 0
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 ?!?!?!
 
Old 02-13-2013, 01:28 PM   #7
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014.08, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,981

Rep: Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610
#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
 
Old 02-13-2013, 01:32 PM   #8
John VV
Guru
 
Registered: Aug 2005
Posts: 13,082

Rep: Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747
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

Last edited by John VV; 02-13-2013 at 01:51 PM. Reason: -- fixed typo
 
1 members found this post helpful.
Old 02-13-2013, 01:56 PM   #9
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014.08, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,981

Rep: Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610Reputation: 2610
# 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".)

-

Last edited by knudfl; 02-13-2013 at 01:58 PM.
 
Old 02-13-2013, 02:06 PM   #10
John VV
Guru
 
Registered: Aug 2005
Posts: 13,082

Rep: Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747Reputation: 1747
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
 
Old 02-14-2013, 03:16 AM   #11
hanamilani
Member
 
Registered: Dec 2008
Posts: 66

Original Poster
Rep: Reputation: 0
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...
 
  


Reply

Tags
xcrysden


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off


Similar Threads
Thread Thread Starter Forum Replies Last Post
xcrysden installation maliksaeed Linux - Enterprise 1 01-06-2013 09:58 AM
The problem for the intallation of xcrysden! stonezhj Linux - Software 1 09-06-2012 03:45 PM
Problem with K path selection in xcrysden bedamani Linux - Newbie 0 09-04-2012 02:43 AM
[SOLVED] xcrysden problem somy Linux - Software 2 12-25-2010 05:15 PM
xcrysden visual somy Linux - Newbie 0 11-24-2010 12:22 AM


All times are GMT -5. The time now is 10:41 AM.

Main Menu
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
identi.ca: @linuxquestions
Facebook: linuxquestions Google+: linuxquestions
Open Source Consulting | Domain Registration