LAM-MPI

[szilagyics]

Hello All,

I have problem with LAM-MPI in linux (ubuntu).
I have never use it before.

When I would like to run lamboot it write me :
************************************************************************************************
szicsa@szicsa-desktop:~$ lamboot -v

LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University

Executing hboot on n0 (localhost - 1 CPU)...
-----------------------------------------------------------------------------
lamboot encountered some error (see above) during the boot process,
and will now attempt to kill all nodes that it was previously able to
boot (if any).

Please wait for LAM to finish; if you interrupt this process, you may
have LAM daemons still running on remote nodes.
-----------------------------------------------------------------------------
wipe ...

LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University

Executing tkill on n0 (localhost)...
szicsa@szicsa-desktop:~$
***********************************************************************************
And when I would like to run mpirun it write me:
******************************************************************************************************
szicsa@szicsa-desktop:~$ mpirun -np 2 /home/szicsa/NIST/FDS/
fds5mpi_linux activate_vents.fds
-----------------------------------------------------------------------------
It seems that there is no lamd running on this host, which indicates
that the LAM/MPI runtime environment is not operating. The LAM/MPI
runtime environment is necessary for the "mpirun" command.

Please run the "lamboot" command the start the LAM/MPI runtime
environment. See the LAM/MPI documentation for how to invoke
"lamboot" across multiple machines.
-----------------------------------------------------------------------------
szicsa@szicsa-desktop:~$


******************************************************************************************************
I installed with alien command the http://www.lam-mpi.org/download/files/lam-6.5.9-tcp.1.i386.rpm
file.

I think I wrong anything. Maybe I didn't install the best file, or I
didn't use good parameters with lamboot.

Could you give me a check list or advices step by step.

Many thanks,
Csaba

[Alexander Ramlow]

use LAM-MPI 7.1.2 and use a host file if you want more than your local
machine ... check which version of MPI has been used to compile FDS.
there are differences in the libraries and that can cause you problems

make sure you got SSH setup for password less authentication for a
non-root account

have NFS working properly with good network connections

[szilagyics]

Alexander,

First: Thank you for your fast answer.

I tried to use LAM-MPI 7.1.4 (in source code) but when I would like to
configure(./configure) it. I got an error message that I haven't got
fortran compiler.
I used the lam-mpi 6.5.9 version because of it was in rpm package.
Sorry, I didn't find 7.1.2 or 7.1.4 in rpm or deb package.
I have searched fortran compiler, but I have found many types of it. I
don't know which is the best for me, and how can I use it.
Sorry, I haven't got any practice from linux mpi ( before I just used
windows mpi with MPICH2).Sorry, I don't know what is the SSH setup.

Thanks for your help,

Csaba

> > I installed with alien command thehttp://www.lam-mpi.org/download/files/lam-6.5.9-tcp.1.i386.rpm

[szilagyics]

I have used the FDS5 in linux platform, but I haven't needed the
fortran compiler because the current fds5-linux is working well in my
ubuntu.
So my problem is the mpi in linux.

Csaba

[Alexander Ramlow]

use

./configure --with-rsh="ssh" --without-fortran

not sure about the fortran part, but it's something along those lines. It will then not compile fortran into lam-mpi. You won't need the fortran compiler to run FDS, but you will need it to compile FDS, even though you can use GCC 4.x as it can handle compiling FDS ... done it before.

Again - doing MPI under linux is not easy and will take a lot of work to get it working, if one has never been exposed to linux at such a level. for some people Windows might be the better option, but in the long run Linux is a better option. I'm even sick of tinkering around with it all, because there are always things that pop up and need your attention. We just put that problem onto someone else externally :o)



cheers

Alexander Ramlow

[szilagyics]

I have found an g77 compiler, and I just have installed succesfully
the LAM-MPI 7.1.4 on one computer. My questions:
I need install the LAN-MPI all of my computers?
I have read in FDS Users guide the lamboot guarantee the connection
beetwen the computers. How can I set the lamboot?

Thanks Csaba

On máj. 26, 10:38, Alexander Ramlow <a...@ramlow.com.au> wrote:
> use
> ./configure --with-rsh="ssh" --without-fortran
> not sure about the fortran part, but it's something along those lines. It will then not compile fortran into lam-mpi. You won't need the fortran compiler to run FDS, but you will need it to compile FDS, even though you can use GCC 4.x as it can handle compiling FDS ... done it before.
> Again - doing MPI under linux is not easy and will take a lot of work to get it working, if one has never been exposed to linux at such a level. for some people Windows might be the better option, but in the long run Linux is a better option. I'm even sick of tinkering around with it all, because there are always things that pop up and need your attention. We just put that problem onto someone else externally :o)
> cheers
> Alexander Ramlow

> szilagyics wrote:I have used the FDS5 in linux platform, but I haven't needed the fortran compiler because the current fds5-linux is working well in my ubuntu. So my problem is the mpi in linux. Csaba On máj. 26, 09:51, szilagyics<csaba.szila...@gmail.com>wrote:Alexander, First: Thank you for your fast answer. I tried to use LAM-MPI 7.1.4 (in source code) but when I would like to configure(./configure) it. I got an error message that I haven't got fortran compiler. I used the lam-mpi 6.5.9 version because of it was in rpm package. Sorry, I didn't find 7.1.2 or 7.1.4 in rpm or deb package. I have searched fortran compiler, but I have found many types of it. I don't know which is the best for me, and how can I use it. Sorry, I haven't got any practice from linux mpi ( before I just used windows mpi with MPICH2).Sorry, I don't know what is the SSH setup. Thanks for your help, Csaba On máj. 26, 07:52, Alexander Ramlow<a...@ramlow.com.au>wrote:use LAM-MPI 7.1.2 and use a host file if you want more than your local machine ... check which version of MPI has been used to compile FDS. there are differences in the libraries and that can cause you problemsmake sure you got SSH setup for password less authentication for a non-root accounthave NFS working properly with good network connectionsszilagyics wrote:Hello All,I have problem with LAM-MPI in linux (ubuntu). I have never use it before.When I would like to run lamboot it write me : ************************************************************************************************ szicsa@szicsa-desktop:~$ lamboot -vLAM 6.5.9/MPI 2 C++/ROMIO - Indiana UniversityExecuting hboot on n0 (localhost - 1 CPU)... ----------------------------------------------------------------------------- lamboot encountered some error (see above) during the boot process, and will now attempt to kill all nodes that it was previously able to boot (if any).Please wait for LAM to finish; if you interrupt this process, you may have LAM daemons still running on remote nodes. ----------------------------------------------------------------------------- wipe ...LAM 6.5.9/MPI 2 C++/ROMIO - Indiana UniversityExecuting tkill on n0 (localhost)... szicsa@szicsa-desktop:~$ *********************************************************************************** And when I would like to run mpirun it write me: ****************************************************************************************************** szicsa@szicsa-desktop:~$ mpirun -np 2 /home/szicsa/NIST/FDS/ fds5mpi_linux activate_vents.fds ----------------------------------------------------------------------------- It seems that there is no lamd running on this host, which indicates that the LAM/MPI runtime environment is not operating. The LAM/MPI runtime environment is necessary for the "mpirun" command.Please run the "lamboot" command the start the LAM/MPI runtime environment. See the LAM/MPI documentation for how to invoke "lamboot" across multiple machines. ----------------------------------------------------------------------------- szicsa@szicsa-desktop:~$****************************************************************************************************** I installed with alien command thehttp://www.lam-mpi.org/download/files/lam-6.5.9-tcp.1.i386.rpm file.I think I wrong anything. Maybe I didn't install the best file, or I didn't use good parameters with lamboot.Could you give me a check list or advices step by step.Many thanks, Csaba

[Alexander Ramlow]

you need to install lam-mpi on all machines, establish passwordless authentication between the machines and once lamboot has successfully started you can see all machines by using lamnodes.

cheers

Alexander Ramlow

szilagyics wrote:

I have found an g77 compiler, and I just have installed succesfully
the LAM-MPI 7.1.4 on one computer. My questions:
I need install the LAN-MPI all of my computers?
I have read in FDS Users guide the lamboot guarantee the connection
beetwen the computers. How can I set the lamboot?

Thanks Csaba


On máj. 26, 10:38, Alexander Ramlow <a...@ramlow.com.au> wrote:
  

use
./configure --with-rsh="ssh" --without-fortran
not sure about the fortran part, but it's something along those lines. It will then not compile fortran into lam-mpi. You won't need the fortran compiler to run FDS, but you will need it to compile FDS, even though you can use GCC 4.x as it can handle compiling FDS ... done it before.
Again - doing MPI under linux is not easy and will take a lot of work to get it working, if one has never been exposed to linux at such a level. for some people Windows might be the better option, but in the long run Linux is a better option. I'm even sick of tinkering around with it all, because there are always things that pop up and need your attention. We just put that problem onto someone else externally :o)
cheers
Alexander Ramlow
szilagyics wrote:I have used the FDS5 in linux platform, but I haven't needed the fortran compiler because the current fds5-linux is working well in my ubuntu. So my problem is the mpi in linux. Csaba On máj. 26, 09:51, szilagyics<csaba.szila...@gmail.com>wrote:Alexander, First: Thank you for your fast answer. I tried to use LAM-MPI 7.1.4 (in source code) but when I would like to configure(./configure) it. I got an error message that I haven't got fortran compiler. I used the lam-mpi 6.5.9 version because of it was in rpm package. Sorry, I didn't find 7.1.2 or 7.1.4 in rpm or deb package. I have searched fortran compiler, but I have found many types of it. I don't know which is the best for me, and how can I use it. Sorry, I haven't got any practice from linux mpi ( before I just used windows mpi with MPICH2).Sorry, I don't know what is the SSH setup. Thanks for your help, Csaba On m&aac
ute;j. 26, 07:52, Alexander Ramlow<a...@ramlow.com.au>wrote:use LAM-MPI 7.1.2 and use a host file if you want more than your local machine ... check which version of MPI has been used to compile FDS. there are differences in the libraries and that can cause you problemsmake sure you got SSH setup for password less authentication for a non-root accounthave NFS working properly with good network connectionsszilagyics wrote:Hello All,I have problem with LAM-MPI in linux (ubuntu). I have never use it before.When I would like to run lamboot it write me : ************************************************************************************************ szicsa@szicsa-desktop:~$ lamboot -vLAM 6.5.9/MPI 2 C++/ROMIO - Indiana UniversityExecuting hboot on n0 (localhost - 1 CPU)... ----------------------------------------------------------------------------- lamboot encountered some error (see above) during the boo
t process, and will now attempt to kill all nodes that it was previously able to boot (if any).Please wait for LAM to finish; if you interrupt this process, you may have LAM daemons still running on remote nodes. ----------------------------------------------------------------------------- wipe ...LAM 6.5.9/MPI 2 C++/ROMIO - Indiana UniversityExecuting tkill on n0 (localhost)... szicsa@szicsa-desktop:~$ *********************************************************************************** And when I would like to run mpirun it write me: ****************************************************************************************************** szicsa@szicsa-desktop:~$ mpirun -np 2 /home/szicsa/NIST/FDS/ fds5mpi_linux activate_vents.fds ----------------------------------------------------------------------------- It seems that there is no lamd running on this host, which indicates that the LAM/MPI runtime environment is not operating. The LAM/MPI runtime environment is necessary for th
e "mpirun" command.Please run the "lamboot" command the start the LAM/MPI runtime environment. See the LAM/MPI documentation for how to invoke "lamboot" across multiple machines. ----------------------------------------------------------------------------- szicsa@szicsa-desktop:~$****************************************************************************************************** I installed with alien command thehttp://www.lam-mpi.org/download/files/lam-6.5.9-tcp.1.i386.rpm file.I think I wrong anything. Maybe I didn't install the best file, or I didn't use good parameters with lamboot.Could you give me a check list or advices step by step.Many thanks, Csaba
    

[szilagyics]

I have installed lammpi on two computer. But when I run lamboot -v it
show me
**********************************************
szicsa@szicsa-desktop:~$ lamboot -v

LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University

n-1<6471> ssi:boot:base:linear: booting n0 (localhost)
n-1<6471> ssi:boot:base:linear: finished
szicsa@szicsa-desktop:~$
******************************************
It's seems its couldn't see another computer. How do I need the NFS.
Which librarys do I have to share?

Thanks,

Csaba

[Kevin]

You need to create a file, for example, lamboot_file. In this file,
enter the names of your computers:

machine1
machine2
machine3
...
...

Then do this

lamboot -v lamboot_file

If you just do a lamboot -v, then LAM/MPI just assumes you want to use
only the current computer. -v just means "verbose", meaning show all
diagnostics.

[szilagyics]

Kevin,

Thanks for your help.

It was very great.

I have installed the lammpi on both computer with --with-rsh="ssh"
flag.
I have created lamboot_file with our two computer, and lamboot can
start, but when I try to run lamboot its write me an error message
that the port22 conection refused. The message was:
******************************************************************
szicsa@szicsa-desktop:~/lenyeg/lammpi/lam-7.1.4$ lamboot -v
lamboot_file

LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University

n-1<8362> ssi:boot:base:linear: booting n0 (szicsa-desktop.mshome)
n-1<8362> ssi:boot:base:linear: booting n1 (szicsa-laptop.mshome)
ERROR: LAM/MPI unexpectedly received the following on stderr:
ssh: connect to host szicsa-laptop.mshome port 22: Connection refused
-----------------------------------------------------------------------------
LAM failed to execute a process on the remote node "szicsa-
laptop.mshome".
LAM was not trying to invoke any LAM-specific commands yet -- we were
simply trying to determine what shell was being used on the remote
host.

LAM tried to use the remote agent command "ssh"
to invoke "echo $SHELL" on the remote node.

*** PLEASE READ THIS ENTIRE MESSAGE, FOLLOW ITS SUGGESTIONS, AND
*** CONSULT THE "BOOTING LAM" SECTION OF THE LAM/MPI FAQ
*** (http://www.lam-mpi.org/faq/) BEFORE POSTING TO THE LAM/MPI USER'S
*** MAILING LIST.

This usually indicates an authentication problem with the remote
agent, some other configuration type of error in your .cshrc or
.profile file, or you were unable to executable a command on the
remote node for some other reason. The following is a list of items
that you should check on the remote node:

- You have an account and can login to the remote machine
- Incorrect permissions on your home directory (should
probably be 0755)
- Incorrect permissions on your $HOME/.rhosts file (if you are
using rsh -- they should probably be 0644)
- You have an entry in the remote $HOME/.rhosts file (if you
are using rsh) for the machine and username that you are
running from
- Your .cshrc/.profile must not print anything out to the
standard error
- Your .cshrc/.profile should set a correct TERM type
- Your .cshrc/.profile should set the SHELL environment
variable to your default shell

Try invoking the following command at the unix command line:

ssh szicsa-laptop.mshome -n 'echo $SHELL'

You will need to configure your local setup such that you will *not*
be prompted for a password to invoke this command on the remote node.
No output should be printed from the remote node before the output of
the command is displayed.

When you can get this command to execute successfully by hand, LAM
will probably be able to function properly.

*********************************************************************

It seems like to me the ubuntu's iptables is not perfect.
I have tired two type of iptables, but in both case the error message
were the same.


first:
***************************************************************
# Generated by iptables-save v1.3.6 on Tue May 27 16:30:15 2008
*filter

COMMIT
# Completed on Tue May 27 16:30:15 2008
*****************************************************************

second:
****************************************************************
# Generated by iptables-save v1.3.6 on Tue May 27 16:30:15 2008
*filter
:INPUT ACCEPT [12:1807]
:FORWARD ACCEPT [0:1000]
:OUTPUT ACCEPT [8:718]
COMMIT
# Completed on Tue May 27 16:30:15 2008
*********************************************************

Thanks, for your help.

Csaba

[szilagyics]

Hello,

I have solved this problem. The problem was that the SSH was missing
from my ubuntu. I could installed it sudo apt-get install ssh. But
there is the new problem:
**********************************************************************************

szicsa@szicsa-desktop:~/lenyeg/lammpi/lam-7.1.4$ lamboot -v
lamboot_file

LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University

n-1<8665> ssi:boot:base:linear: booting n0 (szicsa-desktop.mshome)
n-1<8665> ssi:boot:base:linear: booting n1 (szicsa-laptop.mshome)
szi...@szicsa-laptop.mshome's password:
szi...@szicsa-laptop.mshome's password: ERROR: LAM/MPI unexpectedly

received the following on stderr:

Permission denied, please try again.

*****************************************************************************

I don't know what the password is? I tried the root password but is
not enough good.

Csaba

[Bryan Klein]

Most distributions of Linux will not let you ssh directly as the root user.
You should be connecting as a normal user anyway, root is not required.

You need to ensure that the same user&password is on all machines and you should setup shared keys instead of user/pass authentication for that user.

http://www.debuntu.org/ssh-key-based-authentication

-Bryan

--
Bryan Klein
bryan...@nist.gov

National Institute of Standards and Technology
100 Bureau Drive, Mail Stop 8663
Gaithersburg MD 20899
Phone: 301 975 5171
Fax: 301 975 4052

[szilagyics]

Hello Bryan,

Your help was very good.

I found a site: http://www.cyberciti.biz/tips/linux-multiple-ssh-key-based-authentication.html

It's very simple explain.

So the lamboot works well,but mpirun gives me an error message:
*********************************************************************
szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 /home/szicsa/NIST/FDS/
fds5mpi_linux /home/szicsa/NIST/FDS/activate_vents.fds
mpirun: cannot start /home/szicsa/NIST/FDS/fds5mpi_linux on n0 (o): No
such file or directory
*****************************************************************************

I don't know which file is problem file? I have tried it than I copied
the case file in FDS5mpi_linux's folder, but the problem is same.

Thanks, for you

Csaba

On máj. 27, 18:18, "Bryan Klein" <bryanwkl...@gmail.com> wrote:
> Most distributions of Linux will not let you ssh directly as the root user.
> You should be connecting as a normal user anyway, root is not required.
>
> You need to ensure that the same user&password is on all machines and you
> should setup shared keys instead of user/pass authentication for that user.
>
> http://www.debuntu.org/ssh-key-based-authentication
>
> -Bryan
>

> On Tue, May 27, 2008 at 11:56 AM, szilagyics <csaba.szila...@gmail.com>

> bryan.kl...@nist.gov

[Kevin]

Are you sure you have the name right? fds5mpi_linux?

On May 27, 1:56 pm, szilagyics <csaba.szila...@gmail.com> wrote:
> Hello Bryan,
>
> Your help was very good.
>

> I found a site:http://www.cyberciti.biz/tips/linux-multiple-ssh-key-based-authentica...

>
> It's very simple explain.
>
> So the lamboot works well,but mpirun gives me an error message:
> *********************************************************************
> szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 /home/szicsa/NIST/FDS/
> fds5mpi_linux /home/szicsa/NIST/FDS/activate_vents.fds
> mpirun: cannot start /home/szicsa/NIST/FDS/fds5mpi_linux on n0 (o): No
> such file or directory

> ***************************************************************************­**

>
> I don't know which file is problem file? I have tried it than I copied
> the case file in FDS5mpi_linux's folder, but the problem is same.
>
> Thanks, for you
>
> Csaba
>
> On máj. 27, 18:18, "Bryan Klein" <bryanwkl...@gmail.com> wrote:
>
>
>
> > Most distributions of Linux will not let you ssh directly as the root user.
> > You should be connecting as a normal user anyway, root is not required.
>
> > You need to ensure that the same user&password is on all machines and you
> > should setup shared keys instead of user/pass authentication for that user.
>
> >http://www.debuntu.org/ssh-key-based-authentication
>
> > -Bryan
>
> > On Tue, May 27, 2008 at 11:56 AM, szilagyics <csaba.szila...@gmail.com>
> > wrote:
>
> > > Hello,
>
> > > I have solved this problem. The problem was that the SSH was missing
> > > from my ubuntu. I could installed it sudo apt-get install ssh. But
> > > there is the new problem:
>

> > > ***************************************************************************­*******

> > > szicsa@szicsa-desktop:~/lenyeg/lammpi/lam-7.1.4$ lamboot -v
> > > lamboot_file
>
> > > LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University
>
> > > n-1<8665> ssi:boot:base:linear: booting n0 (szicsa-desktop.mshome)
> > > n-1<8665> ssi:boot:base:linear: booting n1 (szicsa-laptop.mshome)
> > > szi...@szicsa-laptop.mshome's password:
> > > szi...@szicsa-laptop.mshome's password: ERROR: LAM/MPI unexpectedly
> > > received the following on stderr:
> > > Permission denied, please try again.
>

> > > ***************************************************************************­**

>
> > > I don't know what the password is? I tried the root password but is
> > > not enough good.
>
> > > Csaba
>
> > > On máj. 27, 17:22, szilagyics <csaba.szila...@gmail.com> wrote:
> > > > Kevin,
>
> > > > Thanks for your help.
>
> > > > It was very great.
>
> > > > I have installed the lammpi on both computer with --with-rsh="ssh"
> > > > flag.
> > > > I have created lamboot_file with our two computer, and lamboot can
> > > > start, but when I try to run lamboot its write me an error message
> > > > that the port22 conection refused. The message was:
> > > > ******************************************************************
> > > > szicsa@szicsa-desktop:~/lenyeg/lammpi/lam-7.1.4$ lamboot -v
> > > > lamboot_file
> > > > LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University
>
> > > > n-1<8362> ssi:boot:base:linear: booting n0 (szicsa-desktop.mshome)
> > > > n-1<8362> ssi:boot:base:linear: booting n1 (szicsa-laptop.mshome)
> > > > ERROR: LAM/MPI unexpectedly received the following on stderr:
> > > > ssh: connect to host szicsa-laptop.mshome port 22: Connection refused
>

> > > ---------------------------------------------------------------------------­--

> > Fax: 301 975 4052- Hide quoted text -
>
> - Show quoted text -

[szilagyics]

Thanks for your speed!

Yes, I'm sure, I have tried it with rename too.
Maybe the folder will be share or anything like in win version?

Thanks

Csaba

[Kevin]

Can all the machines access the working directory? If you logon to
each machine, can you cd to the directory where the input file is?
Also, why do you not type the mpirun command from the same directory
where the input file is located?

> > > - Show quoted text -- Hide quoted text -

[szilagyics]

I tried to run fds5mpi_linux on the first computer, and the missing
fds5mpi_linux file was not on the second computer. After I copyed the
NIST folder with case file on second computer it's running well.
But it's very interesting for me that the "work files" are in second
computer too. I don't know which group of files is good or which smv
file is good? I'm not sure that is good, because in win the "work
files" are just on first computer in Project folder (example).

Csaba

[szilagyics]

Sorry the pervious message, because of my command was: szicsa@szicsa-
desktop:~/NIST/FDS$ mpirun -np 2 !!!!!fds5_linux!!!!!!
activate_vents.fds

So in this case the fds works alone on all of computers independent
each other. I'm very sorry it.

With fds5mpi_linux it was:
*****************************************************************************************-
szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux
activate_vents.fds
fds5mpi_linux: error while loading shared libraries: libaio.so.1:
cannot open shared object file: No such file or directory
fds5mpi_linux: error while loading shared libraries: libaio.so.1:
cannot open shared object file: No such file or directory
*****************************************************************************

Can I access from second computer in first computer working directory?
What type of share (NFS, SMB) I have to use?

Sorry the pervious,

Csaba


csaba

> ...
>
> tovább »

[Kevin]

activate_vents.fds is a single mesh case, and will not run with -np 2

But you have other problems. On our linux cluster, I can login to any
machine and see any other machine's files via cd. I am not challenged
for passwords when I ssh from one machine to another. You need to be
able to do this or else I am not sure how to help you.

On May 27, 2:57 pm, szilagyics <csaba.szila...@gmail.com> wrote:
> Sorry the pervious message, because of my command was: szicsa@szicsa-
> desktop:~/NIST/FDS$ mpirun -np 2 !!!!!fds5_linux!!!!!!
> activate_vents.fds
>
> So in this case the fds works alone on all of computers independent
> each other. I'm very sorry it.
>
> With fds5mpi_linux it was:

> ***************************************************************************­**************-

> szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux
> activate_vents.fds
> fds5mpi_linux: error while loading shared libraries: libaio.so.1:
> cannot open shared object file: No such file or directory
> fds5mpi_linux: error while loading shared libraries: libaio.so.1:
> cannot open shared object file: No such file or directory

> ***************************************************************************­**

> > > > > > > > > # Completed on Tue May 27 16:30:15 2008- Hide quoted text -
>
> - Show quoted text -...
>
> read more »

[szilagyics]

Many many thanks for your help.

The last problem was that I have to install all of computer the: sudo
apt-get install libaio-dev.

The finish was :
************************************************************************************

szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux
activate_vents.fds

Process 0 of 1 is running on szicsa-laptop
Process 1 of 1 is running on szicsa-desktop
Mesh 1 is assigned to Process 0
Mesh 2 is assigned to Process 1

Fire Dynamics Simulator

Compilation Date : Sat, 10 May 2008
Version : 5.1.6 Parallel
SVN Revision No. : 1673

Job TITLE : Test of VENT activation/deactivation, SVN
$Revision: 935 $
Job ID string : activate_vents

Time Step: 1, Simulation Time: 0.05 s
Time Step: 2, Simulation Time: 0.10 s
Time Step: 3, Simulation Time: 0.15 s
Time Step: 4, Simulation Time: 0.20 s
Time Step: 5, Simulation Time: 0.25 s
*****************************************************************************

> ...
>
> tovább »

[Glenn Forney]

here is a csh script that I run to test whether my ssh connections are
working . fire70 -> fire74 are names of computers on our network. If
things are working then the script loops through each host between the
parens printing out the date on each. If I am asked for a password then
I know there is something wrong with the ssh keys.

#/bin/csh -f
foreach host (fire70 fire71 fire72 fire73 fire74)
echo ""
echo $host
ssh $host date
end

--
Glenn Forney

National Institute of Standards and Technology

100 Bureau Drive, Stop 8663
Gaithersburg MD 20899-8663

Telephone: (301) 975 2313
FAX: (301) 975 4052

Pre-decisional and sensitive information. Not for attribution, distribution, or reproduction.

[Kevin]

Now that wasn't so hard, was it ;)

On May 27, 3:20 pm, szilagyics <csaba.szila...@gmail.com> wrote:
> Many many thanks for your help.
>
> The last problem was that I have to install all of computer the: sudo
> apt-get install libaio-dev.
>
> The finish was :

> ***************************************************************************­*********

> szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux
> activate_vents.fds
> Process   0 of   1 is running on szicsa-laptop
> Process   1 of   1 is running on szicsa-desktop
> Mesh   1 is assigned to Process   0
> Mesh   2 is assigned to Process   1
>
>  Fire Dynamics Simulator
>
>  Compilation Date : Sat, 10 May 2008
>  Version          : 5.1.6 Parallel
>  SVN Revision No. : 1673
>
>  Job TITLE        : Test of VENT activation/deactivation, SVN
> $Revision: 935 $
>  Job ID string    : activate_vents
>
>  Time Step:      1,    Simulation Time:      0.05 s
>  Time Step:      2,    Simulation Time:      0.10 s
>  Time Step:      3,    Simulation Time:      0.15 s
>  Time Step:      4,    Simulation Time:      0.20 s
>  Time Step:      5,    Simulation Time:      0.25 s

> ***************************************************************************­**

>
> On máj. 27, 20:57, szilagyics <csaba.szila...@gmail.com> wrote:
>
>
>
> > Sorry the pervious message, because of my command was: szicsa@szicsa-
> > desktop:~/NIST/FDS$ mpirun -np 2 !!!!!fds5_linux!!!!!!
> > activate_vents.fds
>
> > So in this case the fds works alone on all of computers independent
> > each other. I'm very sorry it.
>
> > With fds5mpi_linux it was:

> > ***************************************************************************­**************-

> > szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux
> > activate_vents.fds
> > fds5mpi_linux: error while loading shared libraries: libaio.so.1:
> > cannot open shared object file: No such file or directory
> > fds5mpi_linux: error while loading shared libraries: libaio.so.1:
> > cannot open shared object file: No such file or directory

> > ***************************************************************************­**

> > > > > > > > > > be prompted for a- Hide quoted text -
>
> - Show quoted text -...
>
> read more »

[szilagyics]

Hello All,

It's very good that computers works in parallel mode in linux.

Can I use with mpirun the Core 2 Duo processor's two core. Do I have
to determine the cores seperate, or mpirun does it automatically?

Csaba

> ...
>
> tovább »

[Kevin]

Do this

mpirun n0 n0 ...

instead of

mpirun -np 2

if you want to just use the machine n0. There is nothing special about
n0. Type

lamnodes

and you will see how each computer is mapped to the n's. While the job
is running, login to the machine and do a

top

and you should see both processes and how the machine is allocating
resources for them.

> > > > > > > > > > > >           probably be 0755)- Hide quoted text -

[Alexander Ramlow]

i think it should be used more like

> mpirun n0,0,0,1,1,1,2,2,2 and so on

where the 0, 1, 2 and so on are the node numbers that you get from

> lamnodes

little hint - FDS will alocate the CPUs to the meshes as per order in the input file. that means, if you have a 3x3 grid of meshes and you described them in the input file row by row along the x-axis and then move to the next row in the y direction until you filled on level and then you go to the next level in z-direction.

say the mesh is like this:

x1y1 - x2y1 - x3y1
x1y2 - x2y2 - x3y2
x1y3 - x2y3 - x3y3

if you alocate the mesh as per the above mpirun line, then machine n0 will get the meshes x1y1, x2y1 and x3y1 - so the top row, n1 will get the second row and n3 the last row. This will work without a problem, but for the performance tuning freaks (like myself) this can be optimised by asigning the meshes in an L-shape like this

n0:

x1y1 - x2y1
x1y2

n1:

           x2y2
x1y3 - x2y3

n3:

x3y1
x3y2
x3y3

reason for that is that the mesh to mesh communication will be more within one machine and less across the network! even though the above example is so simple, that there won't be any difference - it starts making a difference if you got more than 4 meshes assigned to one machine.

say you got  a lot of rows, columns and layers of meshes (like a 4x4x4 rubiks cube or bigger!). picking a mesh in the middle somewhere that has 6 other meshes attached to it (all faces) then you should have all the other 6 meshes running on the same box!

there is a difference if you run like 50+ meshes on some good kit :o)

Alex

[Kevin]

I did not know that you can invoke use this syntax --

mpirun n0,0,1,...

I guess it is easy enough to try it and find out.

Have you tested this idea of assigning meshes? We have not been able
to confirm that communication is made more efficient if it is within
one machine. That is an interesting idea and might be useful to
others.

> Kevin wrote:Do this mpirun n0 n0 ... instead of mpirun -np 2 if you want to just use the machine n0. There is nothing special about n0. Type lamnodes and you will see how each computer is mapped to the n's. While the job is running, login to the machine and do a top and you should see both processes and how the machine is allocating resources for them. On May 28, 12:24 am, szilagyics<csaba.szila...@gmail.com>wrote:Hello All, It's very good that computers works in parallel mode in linux. Can I use with mpirun the Core 2 Duo processor's two core. Do I have to determine the cores seperate, or mpirun does it automatically? Csaba On máj. 27, 21:47, Kevin<mcgra...@gmail.com>wrote:Now that wasn't so hard, was it ;)On May 27, 3:20 pm, szilagyics<csaba.szila...@gmail.com>wrote:Many many thanks for your help.The last problem was that I have to install all of computer the: sudo apt-get install libaio-dev.The finish was : ***************************************************************************­­********* szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux activate_vents.fds Process   0 of   1 is running on szicsa-laptop Process   1 of   1 is running on szicsa-desktop Mesh   1 is assigned to Process   0 Mesh   2 is assigned to Process   1 Fire Dynamics Simulator Compilation Date : Sat, 10 May 2008  Version          : 5.1.6 Parallel  SVN Revision No. : 1673 Job TITLE        : Test of VENT activation/deactivation, SVN $Revision: 935 $  Job ID string    : activate_vents Time Step:      1,    Simulation Time:      0.05 s  Time Step:      2,    Simulation Time:      0.10 s  Time Step:      3,    Simulation Time:      0.15 s  Time Step:      4,    Simulation Time:      0.20 s  Time Step:      5,    Simulation Time:      0.25 s ***************************************************************************­­**On máj. 27, 20:57, szilagyics<csaba.szila...@gmail.com>wrote:Sorry the pervious message, because of my command was: szicsa@szicsa- desktop:~/NIST/FDS$ mpirun -np 2 !!!!!fds5_linux!!!!!! activate_vents.fdsSo in this case the fds works alone on all of computers independent each other. I'm very sorry it.With fds5mpi_linux it was: ***************************************************************************­­**************- szicsa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux activate_vents.fds fds5mpi_linux: error while loading shared libraries: libaio.so.1: cannot open shared object file: No such file or directory fds5mpi_linux: error while loading shared libraries: libaio.so.1: cannot open shared object file: No such file or directory ***************************************************************************­­**Can I access from second computer in first computer working directory? What type of share (NFS, SMB) I have to use?Sorry the pervious,CsabacsabaOn máj. 27, 20:31, szilagyics<csaba.szila...@gmail.com>wrote:I tried to run fds5mpi_linux on the first computer, and the missing fds5mpi_linux file was not on the second computer. After I copyed the NIST folder with case file on second computer it's running well. But it's very interesting for me that the "work files" are in second computer too. I don't know which group of files is good or which smv file is good? I'm not sure that is good, because in win the "work files" are just on first computer in Project folder (example).CsabaOn máj. 27, 20:13, Kevin<mcgra...@gmail.com>wrote:...
>
> read more »

[Alexander Ramlow]

well i haven't got any comparison, but that can easily be tested by having a 2 mesh run. First run it on one dual core machine and then run it on two machines. So the 2 meshes are on different machines. The bandwidth between two cores is up in the GB/s where as the network is around MB/s and then again network is far more volatile when it comes to interference etc.

Alex

Kevin wrote:

:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux activate_vents.fds Process   0 of   1 is running on szicsa-laptop Process   1 of   1 is running on szicsa-desktop Mesh   1 is assigned to Process   0 Mesh   2 is assigned to Process   1 Fire Dynamics Simulator Compilation Date : Sat, 10 May 2008  Version          : 5.1.6 Parallel  SVN Revision No. : 1673 Job TITLE        : Test of VENT activation/deactivation, SVN $Revision: 935 $  Job ID string    : activate_vents Time Step:      1,    Simulation Time:      0.05 s  T
ime Step:      2,    Simulation Time:      0.10 s  Time Step:      3,    Simulation Time:      0.15 s  Time Step:      4,    Simulation Time:      0.20 s  Time Step:      5,    Simulation Time:      0.25 s ***************************************************************************­­**On máj. 27, 20:57, szilagyics<csaba.szila...@gmail.com>wrote:Sorry the pervious message, because of my command was: szicsa@szicsa- desktop:~/NIST/FDS$ mpirun -np 2 !!!!!fds5_linux!!!!!! activate_vents.fdsSo in this case the fds works alone on all of computers independent each other. I'm very sorry it.With fds5mpi_linux it was: ***************************************************************************­­**************- szi
csa@szicsa-desktop:~/NIST/FDS$ mpirun -np 2 fds5mpi_linux activate_vents.fds fds5mpi_linux: error while loading shared libraries: libaio.so.1: cannot open shared object file: No such file or directory fds5mpi_linux: error while loading shared libraries: libaio.so.1: cannot open shared object file: No such file or directory ***************************************************************************­­**Can I access from second computer in first computer working directory? What type of share (NFS, SMB) I have to use?Sorry the pervious,CsabacsabaOn máj. 27, 20:31, szilagyics<csaba.szila...@gmail.com>wrote:I tried to run fds5mpi_linux on the first computer, and the missing fds5mpi_linux file was not on the second computer. After I copyed the NIST folder with case file on second computer it's running well. But it's very interesting for me that the "work files" are in second computer too
. I don't know which group of files is good or which smv file is good? I'm not sure that is good, because in win the "work files" are just on first computer in Project folder (example).CsabaOn máj. 27, 20:13, Kevin<mcgra...@gmail.com>wrote:...

read more »
    

[szilagyi csaba]

Hello,

It's sounds very good. I can try it at the weekend.

Have you got anybody lam-mpi experince with duo cores (one processors
with two core in one motherboard) processors not dual ( two processors
in one motherboard) .

Csaba

2008/5/29 Alexander Ramlow <al...@ramlow.com.au>:

--
Szilágyi Csaba
Hungary
5000 Szolnok
Baross G. utca/street 41. C. I./1.
Tel:+36-70-3748812
email: csaba.s...@gmail.com

[Alexander Ramlow]

same thing - lam-mpi doesn't actually see the processors, you tell it in the lam-host file how many CPUs you give each node and it knows it from there. the actual load balancing is then done by the OS

[szilagyics]

Hello,

In Win version I could to determine more than one mesh to one computer
in config file (computer1 3).
If I see well with LAMMPI I can determine just one mesh / one CPU. Is
it true?

Csaba

[Alexander Ramlow]

well with LAM-MPI you do

mpirun -n0,0,0,1,1,1,1,1,1,1,2,2,2,3,4

if each node has only 2 cores then you assign 3 processes to node0, 7 processes to node1, 3 processes to node2 and one process to node3 and node4

same thing as under windows basically, but here you can actually tell which process or mesh has to be handled by what CPU ...

in the config file in windows the distriution works like this:

computer0 3
computer1 7
computer2 3
computer3 1
computer4 1

you could assign it like

computer0 1
computer0 1
computer0 1
computer1 1
computer1 1
computer1 1
computer1 1
computer1 1
computer1 1
computer1 1
computer2 1
computer2 1
computer2 1
computer3 1
computer4 1

this would result in exactly the same allocation. if you now swap the lines around you can then assign each node to a different mesh!

computer0 1
computer2 4
computer0 2
computer3 1

and so on - you see that computer0 appears twice ... go back to an earlier post and then things should make sense - i hope :o)


Alex