Thread: Random, LONG delays when using ssh

this isn't security issue per se, seems people understand ssh found in forum, here am.

running gromacs 4.5.4, package molecular simulations. 1 of ubuntu's supported packages. have 2 nearly-identical computers, amd six-core machines both running ubuntu 11.10 x86_64.

gromacs has multiprocessing-aware version (also on ubuntu's supported software list) uses open mpi communicate between cpu's. have been using multi-cpu version of gromacs on single machine while now. i'm trying harness second machine on ethernet. in other words, i'm trying set little cluster.

according open mpi documentation, need working ssh connection between master machine , slave machines. have installed openssh-server package on slave machine. followed directions here set public encryption key.

once got set up, tried running gromacs-mpi once, crashed. figured should go basics, , test whether ssh connection working.

can log in slave machine shell using ssh, see 3 problems. actually, 2 of these may 2 manifestations of same problem. both involve random, long delays.

1) after type few commands, cursor freezes. can while i'm in middle of typing command. if i'm patient, text typed right cursor froze appear -- might have wait long 3 5 minutes.

2) receive frequent timeouts when log off of ssh, , try log in.

3) finally, still being asked password on each repeated login. thought ssh public key exchange supposed bypass password prompt?

i'm doing @ home on lan. both of machines sitting behind firewall-enabled router. local network traffic absolutely quiet. other functions on these 2 machines, including web browsing, etc. continue function absolutely while these hangups occur. have tried using ssh master computer, both while logged on locally slave computer , while not logged on. doesn't seem make difference. none of directories on either machine encrypted, understand this post can cause issues when trying access public key.

suspect 1 of these long delays occurred when tried use gromacs-mpi, , caused crash.

suggestions? thanks!

well, solved 1 of problems...

posted ladasky

i still being asked password on each repeated login. thought ssh public key exchange supposed bypass password prompt?

it turns out copied master machine's private key (id_dsa) authorized_hosts file of slave machine rather public key (id_dsa.pub). names similar , missed fact didn't include .pub extension.

i'm still having problem long delays, though. in fact i've seem hanging can occur when slave machine sending me text, not when i'm typing.

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