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" > > 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.
