Hi, all.
I'm new to LIGGGHTS and Linux OS.
When I follow the Installation Tutorial to install LIGGGHTS, I get a problem.
My OS is Fedora 16.
1. when typing "which mpirun"
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/usr/bin/which: no mpirun in (/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/jian/.local/bin:/home/jian/bin)
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The above information is right? or openmpi is not installed well?
2. in /src directory, type "make clean-all", then "make fedora -j"
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grep: angle_*.h: No such file or directory
grep: dihedral_*.h: No such file or directory
grep: improper_*.h: No such file or directory
make[1]: Entering directory `/home/jian/Downloads/LIGGGHTS-PUBLIC/src/Obj_fedora'
mpic++ -g -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -c minimize.cpp
make[1]: mpic++: Command not found
mpic++ -g -O2 -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -DLAMMPS_GZIP -c compute_ke_atom.cpp
make[1]: mpic++: Command not found
make[1]: *** [minimize.o] Error 127
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [compute_ke_atom.o] Error 127
make[1]: Leaving directory `/home/jian/Downloads/LIGGGHTS-PUBLIC/src/Obj_fedora'
make: *** [fedora] Error 2
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How to solve the problems?
Thanks for the help in advance.
ckloss | Wed, 10/03/2012 - 10:26
>>mpic++: Command not
>>mpic++: Command not found
you need to install the openmpi-devel (or openmpi-dev) package
Cheers, Christoph
xujiancqu | Wed, 10/03/2012 - 13:59
I have already installed MPI.
Thanks for your reply.
I have already installed MPI.
--------------------------------------------
[jian@cqu ~]$ sudo yum install openmpi openmpi-devel
[sudo] password for jian:
Loaded plugins: langpacks, presto, refresh-packagekit
Setting up Install Process
Package openmpi-1.5.4-3.fc16.x86_64 already installed and latest version
Package openmpi-devel-1.5.4-3.fc16.x86_64 already installed and latest version
Nothing to do
---------------------------------------------
In addition, symbolic links have been added.
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[jian@cqu ~]$ sudo ln -s /usr/lib64/openmpi/bin/mpirun /usr/bin
ln: failed to create symbolic link `/usr/bin/mpirun': File exists
[jian@cqu ~]$ sudo ln -s /usr/lib64/openmpi/bin/mpic++ /usr/bin
ln: failed to create symbolic link `/usr/bin/mpic++': File exists
-----------------------------------------------
Rds
Jian
xujiancqu | Wed, 10/03/2012 - 14:18
In addition
I used 'find'
--------------------------------------------------------------------
[root@cqu]# find / -name mpirun
find: `/home/jian/.gvfs': Permission denied
/usr/lib64/mpich2/bin/mpirun
/usr/lib64/openmpi/bin/mpirun
/usr/bin/mpirun
--------------------------------------------------------------------
there is /usr/bin/mpirun
why I used 'which'
--------------------------------------------------------------------
[root@cqu]# which mpirun
/usr/bin/which: no mpirun in (/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/jian/.local/bin:/home/jian/bin)
--------------------------------------------------------------------
nasato | Wed, 10/03/2012 - 14:35
Hi Jian, Try to type in the
Hi Jian,
Try to type in the terminal: export PATH=$PATH:/usr/lib/openmpi/bin/
and then try to recompile again.
Best,
Daniel
xujiancqu | Thu, 10/04/2012 - 03:43
Thanks for your
Thanks for your suggestion.
It doesn't work.
Rds
Jian
ckloss | Thu, 10/04/2012 - 10:25
Jian, you can link either
Jian,
you can link either manually or use mpic++ (with the fedora makefile). I you have troubles with either one, I am sure a local linux expert can help you
Christoph
Mallin | Thu, 10/04/2012 - 21:42
Solution: load the modules
Hi Jian,
I also encountered that problem due installation. As mentioned here http://www.openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.1.1/..., you should add the line
module load openmpi-x86_64
to your .bashrc file (you can find it in the home directory).
Worked for me nicely.
Andrew
xujiancqu | Fri, 10/05/2012 - 04:29
Thanks for your
Thanks for your help.
Rds
Jian
tianya4088 | Sun, 06/30/2013 - 14:32
The problem of grep: angle_*.h: No such file or directory
Hi
Jian, I encounter with the same question, once I type "make fedora", then it comes "grep: angle_*.h: No such file or directory
grep: dihedral_*.h: No such file or directory
grep: improper_*.h: No such file or directory
make[1]: Entering directory `/home/jian/Downloads/LIGGGHTS-PUBLIC/src/Obj_fedora'"
Seeing you add an topic on this issue, I want to know how you solve this problem, Thanks
Meng
ckloss | Mon, 07/01/2013 - 10:30
>>grep: angle_*.h: No such
>>grep: angle_*.h: No such file or directory
this is not an error message at all
Cheers
Christoph
rahulsoni | Tue, 09/03/2013 - 14:48
Error 1 in make Fedora
I am trying to install LIGGGTS in Fedora 19 by following the procedure outlined in http://cfdem.dcs-computing.com/?q=node/13
But after doing make clean-all in /src when I perform make fedora then I am getting:
[root@localhost src]# make fedora
make: *** [fedora] Error 1
If anyone can help.
PaulWinkler | Wed, 09/04/2013 - 16:00
Hi,
Hi,
be sure to have full permission on the Liggghts dir. Try changing permissions on the folder or do 'make' as super user.
Regards,
Paul
lbyal | Thu, 09/05/2013 - 09:26
Is the problem solved?
Hi Jian,
Just wondering whether the problem is fixed, Cos I'm currently experiencing the same problem
Regards
Lloyd
AGl | Fri, 09/06/2013 - 07:57
Fix tutorial
Please, fix tutorial on this page:
http://cfdem.dcs-computing.com/?q=node/13
"sudo"-command is used almost everywhere and causes problems. Moreover, it is dangerous to use root-permissions everywhere, where it is not needed.
PaulWinkler | Fri, 09/06/2013 - 19:50
Hi,
Hi,
there are just sudos for ln (/usr/bin needs super user rights) and apt-get/yum which needs root access to. It seems you are afraid of using sudo, can you please tell why this can be dangerous and cause problems? I am using sudo very offense in Ubuntu, because many commands need super user rights.
Best wishes,
Paul
AGl | Mon, 09/09/2013 - 07:43
Sudo
Sorry, my fault. In this tutorial it is really necessary to use "sudo" to install packages.
> + Type "sudo ln -s /path1/src/lmp_fedora /usr/bin/liggghts"
It is potentially dangerous. If you will want to install liggghts from packages later, you will probably get an error, because package manager will not be able to create a binary with the name, which already exists. I am using just the full path "/path1/src/lmp_fedora < in.liggghts_script' for that.
> It seems you are afraid of using sudo, can you please tell why this can be dangerous and cause problems?
I am not afraid, but it is a reliable way to break your system soon. With root-permissions you can accidentally write/delete/move some files in system folders e.g. /usr/bin, /usr/lib etc. And starting your scripts under the root-user is also not the best way of work. Try to escape that.