AMBER Archive (2009)

Subject: [AMBER] Compiling Amber10

From: Williams, John (J.Williams_at_aston.ac.uk)
Date: Tue Sep 22 2009 - 07:56:43 CDT

Hi,
I'm trying to run amber10 on a supermicro machine with 2 Intel QCs and 24GB RAM. Ubuntu 9.04 is installed and all packages are up to date. I'm running it as well on a desktop with 1QC and 4GB RAM. Both machines have the same OS and patch levels. On the desktop it seems to run normally but on the supermicro it goes into a loop calling gettimeofday. This does not seem to related to MPI as the serial version does the same.
Thanks
John
Linux lhs-tesla02 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 19:25:34 UTC 2009 x86_64 GNU/Linux

strace sander -O -i md1.in -o vac_md1.out -p vac.prmtop -c vac_min.crd -r vac_md1.restrt -x vac_md1.mdcrd

Desktop:
open("mdinfo", O_RDWR|O_CREAT, 0666) = 0
dup(0) = 6
close(0) = 0
fstat(6, {st_mode=S_IFREG|0644, st_size=401, ...}) = 0
lseek(6, 0, SEEK_CUR) = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff010bdf40) = -1 ENOTTY (Inappropriate ioctl for device)
write(3, "\n--------------------------------"..., 895) = 895
lseek(6, 0, SEEK_SET) = 0
ftruncate(6, 0) = 0
write(6, "\n NSTEP = 0 TIME(PS) = "..., 81) = 81
lseek(6, 81, SEEK_SET) = 81

Supermicro:
open("mdinfo", O_RDWR|O_CREAT, 0666) = 0^M
dup(0) = 6^M
close(0) = 0^M
fstat(6, {st_mode=S_IFREG|0644, st_size=401, ...}) = 0^M
lseek(6, 0, SEEK_CUR) = 0^M
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff349466c0) = -1 ENOTTY (Inappropriate ioctl for device)^M
gettimeofday({1253620747, 783584}, {0, 0}) = 0^M
gettimeofday({1253620747, 783652}, {0, 0}) = 0^M
gettimeofday({1253620747, 783673}, {0, 0}) = 0^M
gettimeofday({1253620748, 121956}, {0, 2}) = 0^M
gettimeofday({1253620748, 121976}, {0, 2}) = 0^M
gettimeofday({1253620748, 121993}, {0, 2}) = 0^M
gettimeofday({1253620748, 122011}, {0, 2}) = 0^M
gettimeofday({1253620748, 122030}, {0, 2}) = 0^M
gettimeofday({1253620748, 122051}, {0, 2}) = 0^M
gettimeofday({1253620748, 122071}, {0, 2}) = 0^M
gettimeofday({1253620748, 128271}, {0, 0}) = 0^M
gettimeofday({1253620748, 128289}, {0, 0}) = 0^M
gettimeofday({1253620748, 128324}, {0, 0}) = 0^M
gettimeofday({1253620748, 321181}, {0, 13830554455654793216}) = 0^M 

--
This communication is intended solely for the addressee  The message should not be forwarded to any third party without the agreement of the sender.
--
John Williams
ISA
Aston University

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