Re: [ccp4bb] dog slow ccp4i on 64 OpenSUSE and home is on NFS

Thu, 08 Jan 2009 23:41:15 -0800 

Hi,

you cut the output of strace a little too late at the top:

find the entry syaing open("....) = 3
in order to find out what file cannot be read properly.
You might also check (or send here) the contents of /proc/mounts to see what options the nfs-drive was mounted with.
We also often seem to have problems with OpenSuSE through network home directories, e.g. it can take ages to log in and start the window manager. Unfortunately I have not yet figured out what this is due to. 

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Thu, 8 Jan 2009, Joachim Reichelt wrote:


Dear all,

we have a real slow performance of ccp4i, if:
- homedir is on NFS, here /nero is on a i586 Linux system
- actual system is 64 bit, here OpenSUSE 10.3 on core2quad with 8GB ram

from entering ccp4i to see the gui it takes ~2 minutes.
and any popup/dialogue take the same time
This is 6.1, was the same with 6.02

Same user, same system, home dir shifted to a local disk or
same home, user, but i586 (P4, 1GB) some seconds

I have done an strace to see what is going on and I see a lot of:

lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=248, ...}) = 0
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or directory) 
select(0, NULL, NULL, NULL, {0, 10000}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or directory) 
select(0, NULL, NULL, NULL, {0, 10000}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or directory) 
select(0, NULL, NULL, NULL, {0, 10000}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or directory) 
select(0, NULL, NULL, NULL, {0, 10000}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or directory) 
select(0, NULL, NULL, NULL, {0, 10000}) = 0 (Timeout)
... (32 times repeated)

open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)           = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY (Inappropriate ioctl for device) 
lseek(4, 0, SEEK_END)                   = 351
write(4, "db_get_handler_port: opening loc"..., 38) = 38
close(4)                                = 0
open("/nero/jre/.CCP4/dbccp4i.LOCK", O_RDONLY) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)           = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d6250f0) = -1 ENOTTY (Inappropriate ioctl for device) 
read(4, "port number is:4090", 4096)    = 19
read(4, "", 4077)                       = 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 5
fcntl(5, F_SETFD, FD_CLOEXEC)           = 0
ioctl(5, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY (Inappropriate ioctl for device) 
lseek(5, 0, SEEK_END)                   = 389
write(5, "db_get_handler_port: line from l"..., 63) = 63
...

lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)           = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY (Inappropriate ioctl for device) 
lseek(6, 0, SEEK_END)                   = 8764
write(6, "db_handler_processResponse: invo"..., 54) = 54
close(6)                                = 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)           = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY (Inappropriate ioctl for device) 
lseek(6, 0, SEEK_END)                   = 8818
write(6, "*** REQUEST_LIST: request#9\n", 28) = 28
close(6)                                = 0

and I see a lot of:
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily unavailable) 


--
Joachim

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