On Friday, January 9, 2015 at 6:52:55 PM UTC, Christoph Junghans wrote: > 2015-01-09 9:53 GMT-07:00 abrukhno <[email protected]>: > > Thanks for prompt replying Christoph! > > > > On Friday, January 9, 2015 at 4:31:38 PM UTC, Christoph Junghans wrote: > >> 2015-01-09 8:19 GMT-07:00 abrukhno <[email protected]>: > >> > Hi Votcians, > >> > > >> > Is there any way to suppress outputting the running progress of Gromacs > >> > and Votca tools in inverse.log. This "Reading frame" numbers accumulate > >> > into huge logs, which are hard to check on the fly after a couple of > >> > iterations, especially on clusters. Moreover, it constantly writes to > >> > disk, reducing the performance. > >> There is not easy way, "Reading frame" comes out of libgmx. Looking at > >> printcount_ in src/gmxlib/trxio.c there does not seem to be a way to > >> quiet it. > > > > - That is really inconvenient and annoying. On one of the clusters I am > > using this "feature" does not allow me (in any practical terms) to see > > inverse.log for some minutes (after a dozen or more iterations). I can only > > use "tail" then, while I would prefer "less", but this is not the only my > > concern... > > > >> > I have tried to redirect stderr with "2>/dev/null" (for csg_inverse.sh), > >> > or putting "1>/dev/null 2>/dev/null" for inverse.gromacs.log tag, but > >> > the latter removes the logs altogether, which is not desired. > >> inverse.gromacs.log is a separate log file for gromacs program, but > >> not for csg_inverse itself, so that won't work here. > >> "Reading frame" goes to stderr, but forwarding that to /dev/null, one > >> would loss all other error messages. > >> You might be able to create a post-update script, which does something > >> like: > >> sync && sed -e '/Reading frame/d' -i $CSGLOG > > > > - This could be a solution, if the performance of analysis tools was not > > affected, but writing so often to disk (after every single frame read!) > > should drastically increase the execution time during the reading stage, > > and it does take quite some time - about 20-30 mins for about 10 mln frames > > in trajectory in my latest case (which is relatively light in terms of the > > number of beads). > > > > - may I ask you what "exec 3>&1 4>&2 >> "$CSGLOG" 2>&1" does in > > enable_logging() (functions_common.sh)? I mean I could not find out the > > meaning of file descriptors "3" and "4" (I reckon exec redirects them). > We create two new file descriptors ("3" and "4") and 3 is linked to > 1(stdout) and 4 to 2(stderr), while the current 1 (stdout) is appended > to "$CSGLOG" and the current 2(stderr) is appended to the current 1 > (stdout). > This way, if you do use stdout/stderr in a script it will end up in > the log file and not on the screen, while if you use fd 3,4 will end > up of the screen (that is what 'msg' is doing). > > I guess > exec 3>&1 4>&2 >> "$CSGLOG" 2>/dev/null > will do what you want. > > We could add an option like cg.inverse.error_log_file and use > exec 3>&1 4>&2 >> "$CSGLOG" 2> "$CSG_ERRORLOG"
- that might be useful, but maybe you don't put quotes around $CSG_ERRORLOG ? otherwise, can it create a file named "/dev/null" instead of dumping the output into the null device? I've tried "inverse.log 2>inverse.err" for $CSGLOG (via tag cg.inverse.log_file in settings.xml) and got the file named "inverse.log 2>inverse.err" (without quotes) - out of curiosity, do you ever actually use descriptors 3 and/or 4, or is it there just in case for the future uses? Thanks > > > > Andrey > > > >> Christoph > >> > >> > > >> > Thanks > >> > > >> > Andrey > >> > > >> > > >> > > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, send > >> > an email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at http://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
