Not able to execute matrix multiplication


#21

Yes, It is possible for me to passwordlessly login to system using both
ssh subu@subu-deskto & ssh subu@127.0.0.1


#22

Alright - try the gemm query again. Did you make sure /etc/hosts file is ok and does not have any extraneous entries?


#23

Error showing while executing gemm.

/etc/hosts content listed below

[color=#FF0000]127.0.0.1 localhost
192.168.1.7 subu-desktop

The following lines are desirable for IPv6 capable hosts

::1 ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters[/color]


#24

Let’s look at the logs again, see viewtopic.php?f=11&t=1478#p3403


#25

Please see the tar file [color=#0000FF]all_20141112220950.tar [/color]uploaded via ftp


#26

From the mpi logs it seems like there is still a connection/networking problem. While we are looking for possible resolutions, please run these debugging commands and post all results:
[ul]
[]lsb_release -a[/]
[]sudo ufw status[/]
[]ssh subu-desktop echo test[/]
[/ul]
First command is to check your exact OS version. Second is to check Ubuntu firewall (do you know of any other firewall software running on your machine?) And third is just to re-verify passwordless ssh one more time.


#27

[color=#0000FF]subu@subu-desktop:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.04.5 LTS
Release: 12.04
Codename: precise[/color]

[color=#FF0000]subu@subu-desktop:~$ sudo ufw status
[sudo] password for subu:
Status: inactive[/color]

[color=#4000FF]subu@subu-desktop:~$ ssh subu-desktop echo test
test[/color]


#28

Try running the folllowing:
dpkg -l | grep mpich2

echo subu-desktop > hosts.txt
/opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f hosts -n 4 uname -a
/opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f hosts -n 4 hostname


#29

The output genereated after i had run the commands specified in the previous post is as follows

[color=#FF0000]subu@subu-desktop:~$ dpkg -l | grep mpich2
ii scidb-14.8-libmpich2-1.2 1.2.1.1-4 Shared libraries for MPICH2
ii scidb-14.8-libmpich2-dev 1.2.1.1-4 Development files for MPICH2
ii scidb-14.8-mpich2 1.2.1.1-4 Implementation of the MPI Message Passing Interface standard[/color]

[color=#0000FF]subu@subu-desktop:~$ echo subu-desktop > hosts.txt[/color]

[color=#FF4000]subu@subu-desktop:~$ /opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f hosts -n 4 uname -a
[mpiexec@subu-desktop] HYDU_parse_hostfile (./utils/args/args.c:169): unable to open host file: hosts
[mpiexec@subu-desktop] mfile_fn (./ui/mpiexec/utils.c:195): error parsing hostfile
[mpiexec@subu-desktop] match_arg (./ui/mpiexec/utils.c:1054): match handler returned error
[mpiexec@subu-desktop] HYD_uii_mpx_get_parameters (./ui/mpiexec/utils.c:1262): argument matching returned error

Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : …

Global options (passed to all executables):

Global environment options:
-genv {name} {value} environment variable name and value
-genvlist {env1,env2,…} environment variable list to pass
-genvnone do not pass any environment variables
-genvall pass all environment variables (default)

Other global options:
-f {name} file containing the host names
-wdir {dirname} working directory to use

Local options (passed to individual executables):

Local environment options:
-env {name} {value} environment variable name and value
-envlist {env1,env2,…} environment variable list to pass
-envnone do not pass any environment variables
-envall pass all environment variables (default)

Other local options:
-n/-np {value} number of processes
{exec_name} {args} executable name and arguments

Hydra specific options (treated as global):

Bootstrap options:
-bootstrap bootstrap server to use
-bootstrap-exec executable to use to bootstrap processes
-enable-x/-disable-x enable or disable X forwarding

Proxy options (only needed for persistent mode):
-boot-proxies boot proxies to run in persistent mode
-boot-foreground-proxies boot foreground proxies (persistent mode)
-shutdown-proxies shutdown persistent mode proxies
-proxy-port port for proxies to listen (boot proxies)
-use-persistent use persistent mode proxies to launch

Communication sub-system options:
-css communication sub-system to use

Resource management kernel options:
-rmk resource management kernel to use

Hybrid programming options:
-ranks-per-proc assign so many ranks to each process
-enable/-disable-pm-env process manager environment settings

Process-core binding options:
-binding process-to-core binding mode
-bindlib process-to-core binding library (plpa)

Checkpoint/Restart options:
-ckpoint-interval checkpoint interval
-ckpoint-prefix checkpoint file prefix
-ckpointlib checkpointing library (blcr)
-ckpoint-restart restart a checkpointed application

Other Hydra options:
-verbose verbose mode
-info build information
-print-rank-map print rank mapping
-print-all-exitcodes print exit codes of all processes[/color]

[color=#4000FF]subu@subu-desktop:~$ /opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f hosts -n 4 hostname
[mpiexec@subu-desktop] HYDU_parse_hostfile (./utils/args/args.c:169): unable to open host file: hosts
[mpiexec@subu-desktop] mfile_fn (./ui/mpiexec/utils.c:195): error parsing hostfile
[mpiexec@subu-desktop] match_arg (./ui/mpiexec/utils.c:1054): match handler returned error
[mpiexec@subu-desktop] HYD_uii_mpx_get_parameters (./ui/mpiexec/utils.c:1262): argument matching returned error

Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : …

Global options (passed to all executables):

Global environment options:
-genv {name} {value} environment variable name and value
-genvlist {env1,env2,…} environment variable list to pass
-genvnone do not pass any environment variables
-genvall pass all environment variables (default)

Other global options:
-f {name} file containing the host names
-wdir {dirname} working directory to use

Local options (passed to individual executables):

Local environment options:
-env {name} {value} environment variable name and value
-envlist {env1,env2,…} environment variable list to pass
-envnone do not pass any environment variables
-envall pass all environment variables (default)

Other local options:
-n/-np {value} number of processes
{exec_name} {args} executable name and arguments

Hydra specific options (treated as global):

Bootstrap options:
-bootstrap bootstrap server to use
-bootstrap-exec executable to use to bootstrap processes
-enable-x/-disable-x enable or disable X forwarding

Proxy options (only needed for persistent mode):
-boot-proxies boot proxies to run in persistent mode
-boot-foreground-proxies boot foreground proxies (persistent mode)
-shutdown-proxies shutdown persistent mode proxies
-proxy-port port for proxies to listen (boot proxies)
-use-persistent use persistent mode proxies to launch

Communication sub-system options:
-css communication sub-system to use

Resource management kernel options:
-rmk resource management kernel to use

Hybrid programming options:
-ranks-per-proc assign so many ranks to each process
-enable/-disable-pm-env process manager environment settings

Process-core binding options:
-binding process-to-core binding mode
-bindlib process-to-core binding library (plpa)

Checkpoint/Restart options:
-ckpoint-interval checkpoint interval
-ckpoint-prefix checkpoint file prefix
-ckpointlib checkpointing library (blcr)
-ckpoint-restart restart a checkpointed application

Other Hydra options:
-verbose verbose mode
-info build information
-print-rank-map print rank mapping
-print-all-exitcodes print exit codes of all processes
[/color]


#30

Please run the coorected command:

echo subu-desktop > hosts.txt
/opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f ./hosts.txt -n 4 uname -a
/opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f ./hosts.txt -n 4 hostname


#31

Output obtained while running commands given in the previous post

[color=#0000FF]subu@subu-desktop:~$ echo subu-desktop > hosts.txt
bash: hosts.txt: Read-only file system[/color]

[color=#FF4000]subu@subu-desktop:~$ /opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f ./hosts.txt -n 4 uname -a
Linux subu-desktop 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux subu-desktop 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux subu-desktop 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux subu-desktop 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux[/color]

[color=#8000BF]subu@subu-desktop:~$ /opt/scidb/14.8/3rdparty/mpich2/bin/mpiexec.hydra -f ./hosts.txt -n 4 hostname
subu-desktop
subu-desktop
subu-desktop
subu-desktop[/color]


#32

It still seems like some sort of an ssh problem. What username did you specify for -u switch during the cluster install? Was it scidb or any other username?


#33

subu@subu-desktop:~$ echo subu-desktop > hosts.txt
bash: hosts.txt: Read-only file system
Seems like a problem … looks like you cannot write to ~subu/. Assuming subu is the user under whom scidb runs this is pretty non-standard and we have never tested such an environment. Can you write to /tmp ? (touch /tmp/foo as the user of scidb). If not, that is a problem for sure.
Also, make sure that your iptables and SELinux either configured correctly or turned off. See paradigm4.com/HTMLmanual/14. … 01s02.html.
Anyway, the first step is to make sure that the mpich.hydra command from my previus post works correctly.


#34

Hai,
Thank you for your support. I am planning to reinstall scidb. Last time i followed instructions mentioned in the video presentation found there in the paradigm site for installation. Any additional preparations to be made before the installation? Any suggestions?
Regards
Subu


#35

One thing that may help is to shut down all postgres services other than postgres 8.4. It will help to configure postgres 8.4 during the installation. Otherwise, please follow the instructions for the cluster install located here:
https://github.com/Paradigm4/deployment/tree/master