Hello Phil--
> > I would have posted this to the xplor-nih email list, but I cannot > seem to > access it through the xplor-nih web page. My colleague, Dr. In-Ja > Byeon, > suggested I email you direct with a sort of problem I am having with > xplor-nih. > > To post on the mailing list, you must belong to the mailing list. I'm > CCing this message to the list to make certain that it's actually > working, as I haven't seen messages there for a while myself. > > If you click on the link for the email list or the archive on the xplor-nih > web page you get a time out. My guess is that cake.cit.nih.gov is not online > anymore. or no longer seen from the outside world. Thus I could not even sign > up for the email list. > > http://cake.cit.nih.gov/pipermail/xplor-nih/ > Thanks for the hint. That machine is available to me, but no longer to the outside world. Thanks for pointing that out- I will see what I can do about that. > 2) > > The first issue is that running the xplor command using input file > redirection ( < input.py ) does not seem to produce any .sa output > files. > This is counter to to older instructions that I used for my original > PBS job > script. > ( eg. xplor -py -smp 16 -o anneal_py.out < anneal.py or xplor -py > -parallel > -o anneal_py.out -machines > xplor_machines.6071BFDD51DF41BB144C4A801790DE9E < > anneal.py ) > > Getting rid of the redirection ( < ) from the command line allows > the jobs > to run to completion and create the sa files. I am not sure if this > is a bug > or feature that I issued in one of the upgrades/ change-logs. I just > wanted > to bring this to someone’s attention. Also, even though no sa files > are > produced, there is no significant difference in the time to run the > job with > or without input redirection. > > I generally much prefer direct specification of the script name, > rather than redirection, but when I tried it just now on my machine > here, things worked. However, the output file names were > .xplorInput_0.sa and .xplorInput_1.sa. It's really better not to use > redirection. If you find public documentation suggesting using > redirection, I'd appreciate it if you bring it to my attention, so I > can get it fixed. > > So it was writing out the sa files as hidden files? I did not even check > that. Right. Quite misleading. > > As for where I found the redirection documentation specifically > > http://nmr.cit.nih.gov/xplor-nih/nih/xplor.pbs > Thank you. I have changed that. > linked from the FAQ and a similar script found on the biowulf > xplor-nih page. And I emailed them to fix things there too. Thank you for the email. Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
