On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote: > > On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca > <[email protected] <javascript:>> wrote: > > In this case, it's not an error message which is lost ;) Why does it go > to > > stderr at all? > The code has the reason right there: > #print this message to stderr because $(critical something) is used very > often > > > Moreover, if I try to run the iteration a second time, everything > including > > errors is reported back > Well that is good, nevertheless we just spend 5 E-Mails back and > forth, hunting down a bug you introduced yourself. > And I now recall you made that change to filter gromacs "Read frame > XXX" message, which is fixed when using a newer gromacs version > (>=2016.3), see: > > https://github.com/votca/csg/commit/155eb770873a6f65bac372c9f8c5efc9f3a4be75 > > > > > Anyway, my primary issue is not about messages, but to make it work > > correctly for distributions. > Like I said in the other email if section 7.3.2 is right, a mapping > file might be needed only for IMC, but even that I think is not true > anymore in v1.3.1. >
My test IMC iteration went through without tagging the 1:1 CG map file. > So you need to figure out, which exclusions you want to read the ones > from the mapping file or the ones the tpr. > For the former specify a mapping file or the latter don't. > OK, I preferred the exclusions from topol-rdf.tpr (which appears to work now for IBI), so I skipped the map tags in my settings file for IMC too. However, the distributions are still wrong in the case of IMC. > > And then you can use csg_dump with or without --cg option to check the > exclusions! > $ csg_dump --top topol.tpr --excl > or > $ csg_dump --top topol.tpr --excl --cg mapping.xml. > > Christoph > > > > > Andrey > > > > On Monday, July 23, 2018 at 2:33:44 PM UTC+1, Christoph Junghans wrote: > >> > >> On Mon, Jul 23, 2018 at 7:28 AM, 'Andrey Brukhno' via votca > >> <[email protected]> wrote: > >> > Christoph, > >> > > >> > I think I figured why there is no log msg for critical csg_stat in > >> > calc_rdfgeneric.sh. > >> > The fact is I override the inverse.sh script with the one having this > >> > (to > >> > avoid all the frame numbers when reading trajectory files): > >> > > >> > log="${PWD}/${log##*/}" > >> > export CSGLOG="$log" > >> > if [[ -f $CSGLOG ]]; then > >> > exec 3>&1 4>&2 >> "$CSGLOG" 2>&1 > >> > echo -e "\n\n##################################" > >> > # echo "# Appending to existing logfile #" > >> > echo "# Appending to logfile (+errors) #" > >> > echo -e "##################################\n\n" > >> > msg --color blue "Appending to existing logfile (+errors) > >> > ${CSGLOG##*/}" > >> > else > >> > exec 3>&1 4>&2 >> "$CSGLOG" 2>/dev/null > >> > echo -e "\n\n##################################" > >> > echo "# Creating new logfile (-errors) #" > >> > echo -e "##################################\n\n" > >> > msg "For a more verbose log see: ${CSGLOG##*/} (or > >> > csg_inverse.log)" > >> > fi > >> > > >> > This worked before and did not affect the workflow. > >> Glad, you found it and it is not VOTCA's original code. > >> I remember now that you did this modification for a reason, which I > >> didn't like exactly because error message will get lost. > >> > >> Anyhow, well in conclusion if you send the errors to dev/null, you > >> won't see some messages (like critical) in the log file. > >> > >> Christoph > >> > > >> > Andrey > >> > > >> > On Mon, Jul 23, 2018 at 1:50 PM, Christoph Junghans < > [email protected]> > >> > wrote: > >> >> > >> >> On Mon, Jul 23, 2018 at 6:46 AM, 'Andrey Brukhno' via votca > >> >> <[email protected]> wrote: > >> >> > Sorry, I forgot - below is the output of `grep critical > inverse.log' > >> >> > for > >> >> > one > >> >> > iteration: > >> >> > > >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p > >> >> > topol.top > >> >> > -o topol.tpr -c conf.gro' > >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p > >> >> > topol.top > >> >> > -o topol.tpr -c conf.gro' > >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p > >> >> > topol.top > >> >> > -o topol.tpr -c conf.gro' > >> >> > Running critical command 'gmx grompp -n index.ndx -f grompp.mdp -p > >> >> > topol.top > >> >> > -o topol.tpr -c conf.gro' > >> >> > Running critical command 'mpirun -n 4 mdrun_mpi -s topol.tpr -c > >> >> > confout.gro > >> >> > -o traj.trr -x traj.xtc -cpi state.cpt -maxh 47.8289 -multidir > sim_0 > >> >> > sim_1 > >> >> > sim_2 sim_3 -tablep table.xvg -tableb table_b1.xvg table_b2.xvg > >> >> > table_b3.xvg > >> >> > table_b4.xvg table_b5.xvg table_a1.xvg table_a2.xvg table_a3.xvg > >> >> > table_a4.xvg table_a5.xvg table_d1.xvg table_d2.xvg table_d3.xvg > >> >> > table_d4.xvg table_d5.xvg table_d6.xvg' > >> >> > Doing: critical csg_stat --nt 4 --options > >> >> > > >> >> > > >> >> > > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cNT/dopc_cg-int-map11.xml > > > >> >> > --top topol-rdf.tpr --trj traj.xtc --begin 0 --first-frame 0 > >> >> > --block-length > >> >> > 1000000 --ext dist.block --cg > >> >> > > >> >> > > >> >> > > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cNT/dopc_cg-map11.xml; > > > >> >> > > >> >> > As you can see, the only mention of `critical csg_stat' is due to > my > >> >> > addition of echo. > >> >> Well, the other lines with "Running critical command" show that the > >> >> logging actually works. > >> >> Did you overload calc_rdf_generic.sh with your own version? > >> >> Otherwise, I would say your installation is bourked up. > >> >> > >> >> Christoph > >> >> > > >> >> > Andrey > >> >> > > >> >> > On Monday, July 23, 2018 at 1:17:32 PM UTC+1, Christoph Junghans > >> >> > wrote: > >> >> >> > >> >> >> On Mon, Jul 23, 2018 at 2:39 AM, 'Andrey Brukhno' via votca > >> >> >> <[email protected]> wrote: > >> >> >> > > >> >> >> > On Mon, Jul 23, 2018 at 2:22 AM, Christoph Junghans > >> >> >> > <[email protected]> > >> >> >> > wrote: > >> >> >> >> > >> >> >> >> On Sun, Jul 22, 2018 at 1:27 PM, 'Andrey Brukhno' via votca > >> >> >> >> <[email protected]> wrote: > >> >> >> >> > Thanks for your reply Christoph. > >> >> >> >> > > >> >> >> >> > I did check it, but inverse.log does not contain sufficient > >> >> >> >> > info, > >> >> >> >> > see > >> >> >> >> > the > >> >> >> >> > extract below. > >> >> >> >> > I will be investigating it further to make sure I did not do > >> >> >> >> > anything > >> >> >> >> > stupid > >> >> >> >> > myself, although I haven't changed much for the test > iteration > >> >> >> >> > except > >> >> >> >> > recompiling the tpr files for the newer version of Gromacs). > >> >> >> >> The " rdf calculation is already done" tells me that this is > not > >> >> >> >> a > >> >> >> >> run > >> >> >> >> from scratch. > >> >> >> >> Try a fresh run, because some chance in the xml don't get > >> >> >> >> populated > >> >> >> >> until the next iteration step. > >> >> >> >> And grep for "csg_stat" (not rdf), you should see actually > >> >> >> >> command, > >> >> >> >> which got run, e.g.: > >> >> >> >> "Running critical command 'csg_stat --nt 4 --options > settings.xml > >> >> >> >> --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0' " > >> >> >> >> From that you can see if all the options are read as excepted. > >> >> >> >> > >> >> >> > > >> >> >> > I knew you were going to say this... > >> >> >> > As a matter of fact, there is no such message from > >> >> >> > calc_rdf_generic.sh, > >> >> >> > but > >> >> >> > instead: > >> >> >> > > >> >> >> > msg "Calculating rdfs with csg_stat using $tasks tasks" > >> >> >> > critical csg_stat --nt $tasks --options "$CSGXMLFILE" --top > >> >> >> > "$topol" > >> >> >> > --trj > >> >> >> > "$traj" --begin $equi_time --first-frame $first_frame > >> >> >> > ${error_opts} > >> >> >> > ${maps:+--cg ${maps}} > >> >> >> > mark_done "rdf_calculation${suffix}" > >> >> >> Well the "critical" function includes the print statement: > >> >> >> critical() { > >> >> >> [[ $quiet = "no" ]] && echo "Running critical command '$*'" >&2 > >> >> >> "$@" || die "${FUNCNAME[0]}: '$*' failed" > >> >> >> } > >> >> >> So I am not sure when that got lost in your case. > >> >> >> > > >> >> >> > so I had to add this after the msg and before the csg_stat > call: > >> >> >> > echo "Doing: critical csg_stat --nt $tasks --options > >> >> >> > "$CSGXMLFILE" > >> >> >> > --top > >> >> >> > "$topol" --trj "$traj" --begin $equi_time --first-frame > >> >> >> > $first_frame > >> >> >> > ${error_opts} ${maps:+--cg ${maps}}" > >> >> >> > > >> >> >> > This shows me that topol-rdf.tpr is actually used (extract from > >> >> >> > inverse.log): > >> >> >> > > >> >> >> > Make update for ibi > >> >> >> > Calculating rdfs with csg_stat using 4 tasks > >> >> >> > Doing: critical csg_stat --nt 4 --options > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cT/dopc_cg-int-map11.xml > > > >> >> >> > --top topol-rdf.tpr --trj traj.xtc --begin 0 --first-frame 0 > >> >> >> > --block-length > >> >> >> > 1000000 --ext dist.block --cg > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > /home/andrey/Work/Models/DOPC-long-wtip4p-new/ibi-Rc1.65nm-freeN-dihs_CG-fits1-151cT/dopc_cg-map11.xml; > > > >> >> >> > begin to calculate distribution functions > >> >> >> > > >> >> >> > However, the distributions are still wrong, and I am lost now > as > >> >> >> > to > >> >> >> > which > >> >> >> > program to blame (again all the initial files are the same as > in > >> >> >> > my > >> >> >> > previous > >> >> >> > iteration). > >> >> >> > I compared the outputs of `gmx dump topol-rdf.tpr' and `gmx > dump > >> >> >> > topol.tpr' > >> >> >> > generated with the new Gromacs and everything seems alright, > the > >> >> >> > relevant > >> >> >> > differences in exclusion lists are there. > >> >> >> > The problem is also that the original calculation was done on a > >> >> >> > cluster > >> >> >> > more > >> >> >> > than a year ago, so I cannot reproduce exactly all the > >> >> >> > installation > >> >> >> > setup, > >> >> >> > not on my desktop anyway. But I know that those calculations > were > >> >> >> > correct > >> >> >> > and well converged. > >> >> >> > > >> >> >> > So something should have changed somewhere within the newly > >> >> >> > installed > >> >> >> > Gromacs/VOTCA combination. > >> >> >> You can see what VOTCA has with: > >> >> >> csg_dump --top topol-rdf.tpr --cg dopc_cg-map11.xml > >> >> >> > >> >> >> Remember, if you are using a mapping file ("--cg" option) > exclusions > >> >> >> from the topology file are ignored and the ones from the mapping > >> >> >> file > >> >> >> are used instead. > >> >> >> > >> >> >> Christoph > >> >> >> > > >> >> >> > Andrey > >> >> >> > > >> >> >> >> Christoph > >> >> >> >> > > >> >> >> >> > Andrey > >> >> >> >> > ----- > >> >> >> >> > $ grep rdf inverse.log > >> >> >> >> > ... > >> >> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr > >> >> >> >> > table_??.xvg > >> >> >> >> > index.ndx* conf.gro*' > >> >> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr > >> >> >> >> > table_??.xvg > >> >> >> >> > index.ndx* conf.gro*' > >> >> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr > >> >> >> >> > table_??.xvg > >> >> >> >> > index.ndx* conf.gro*' > >> >> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr > >> >> >> >> > table_??.xvg > >> >> >> >> > index.ndx* conf.gro*' > >> >> >> >> > cp_from_main_dir: 'grompp.mdp* topol.top* topol-rdf.tpr > >> >> >> >> > table_??.xvg > >> >> >> >> > index.ndx* conf.gro*' > >> >> >> >> > ‘sim_0/topol-rdf.tpr’ -> ‘./topol-rdf.tpr’ > >> >> >> >> > Calculating rdfs with csg_stat using 4 tasks > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCH-TCH > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCH-TCO > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCO-TCO > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCH-PO > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCH-NH > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCO-PO > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > TCO-NH > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > PO-PO > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > PO-NH > >> >> >> >> > rdf calculation is already done > >> >> >> >> > Calculating average rdfs and its errors for interaction > NH-NH > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > On Sun, Jul 22, 2018 at 1:26 PM, Christoph Junghans > >> >> >> >> > <[email protected]> > >> >> >> >> > wrote: > >> >> >> >> >> > >> >> >> >> >> On Sat, Jul 21, 2018 at 9:01 PM, 'Andrey Brukhno' via votca > >> >> >> >> >> <[email protected]> wrote: > >> >> >> >> >> > Hello, > >> >> >> >> >> > > >> >> >> >> >> > I encountered a very strange (looks like legacy) issue > with > >> >> >> >> >> > v1.4.1. > >> >> >> >> >> > In my earlier IBI iterations (with v1.3) I normally used > >> >> >> >> >> > special > >> >> >> >> >> > topol-rdf.tpr which was different from normal CG > simulation > >> >> >> >> >> > topol.tpr > >> >> >> >> >> > by > >> >> >> >> >> > not > >> >> >> >> >> > including the intra-molecular pairs in the RDF stats > (done > >> >> >> >> >> > by > >> >> >> >> >> > csg_stat). > >> >> >> >> >> > I > >> >> >> >> >> > wanted to make sure my previous results are reproduced by > >> >> >> >> >> > v1.4.1, > >> >> >> >> >> > so > >> >> >> >> >> > copied > >> >> >> >> >> > all the initialisation files into a new directory and > tried > >> >> >> >> >> > to > >> >> >> >> >> > run > >> >> >> >> >> > once > >> >> >> >> >> > again. After the very first iteration I checked the > obtained > >> >> >> >> >> > RDFs > >> >> >> >> >> > and > >> >> >> >> >> > they > >> >> >> >> >> > were all wrong - corresponding to normal topol.tpr > >> >> >> >> >> > (including > >> >> >> >> >> > intra-pairs) > >> >> >> >> >> > and not topol-rdf.tpr (excluding intra-pairs)! > >> >> >> >> >> > > >> >> >> >> >> > I guess there might have been changes made to locations > or > >> >> >> >> >> > names > >> >> >> >> >> > of > >> >> >> >> >> > tags > >> >> >> >> >> > in > >> >> >> >> >> > settings.xml between the VOTCA versions, but I could not > >> >> >> >> >> > identify > >> >> >> >> >> > those > >> >> >> >> >> > changes by referring to the most recent manual (both > v1.4.1 > >> >> >> >> >> > and > >> >> >> >> >> > development > >> >> >> >> >> > versions). > >> >> >> >> >> > > >> >> >> >> >> > Below is the relevant extract from my settings.xml file. > >> >> >> >> >> > > >> >> >> >> >> > Any clue, hint, advice are most welcome! > >> >> >> >> >> We haven't changes any tags in IBI since v1.4.1 and the > >> >> >> >> >> special > >> >> >> >> >> topology for IBI can be set by > >> >> >> >> >> cg.inverse.<sim_prog>.rdf.topol, > >> >> >> >> >> which > >> >> >> >> >> you did below. > >> >> >> >> >> You could try "grep csg_stat inverse.log" to figure out if > the > >> >> >> >> >> right > >> >> >> >> >> topology got appended to the command line of csg_stat. > >> >> >> >> >> > >> >> >> >> >> Christoph > >> >> >> >> >> > > >> >> >> >> >> > Thanks in advance. > >> >> >> >> >> > Andrey > >> >> >> >> >> > > >> >> >> >> >> > ----------- > >> >> >> >> >> > <gromacs> > >> >> >> >> >> > <grompp> > >> >> >> >> >> > <bin>gmx grompp</bin> > >> >> >> >> >> > <!--opts></opts--> > >> >> >> >> >> > </grompp> > >> >> >> >> >> > <mdrun> > >> >> >> >> >> > <!--command>grmx-vtc-rerun.sh</command--> > >> >> >> >> >> > <!--command>mpirun -lsf mdrun_mpi</command--> > >> >> >> >> >> > <!--opts>-multidir sim_0 sim_1 sim_2 > sim_3</opts--> > >> >> >> >> >> > <command>mpirun -n 4 mdrun_mpi</command> > >> >> >> >> >> > <opts>-multidir sim_0 sim_1 sim_2 sim_3 -tablep > >> >> >> >> >> > table.xvg > >> >> >> >> >> > -tableb > >> >> >> >> >> > table_b?.xvg table_a?.xvg table_d?.xvg</opts> > >> >> >> >> >> > </mdrun> > >> >> >> >> >> > <!--mdrun><opts>-nt 2</opts></mdrun--> > >> >> >> >> >> > <!-- trash so many frames at the beginning --> > >> >> >> >> >> > <equi_time>0</equi_time> > >> >> >> >> >> > <!-- grid for table*.xvg !--> > >> >> >> >> >> > <table_bins>0.001</table_bins> > >> >> >> >> >> > <!-- cut the potential at this value (gromacs bug) > --> > >> >> >> >> >> > <pot_max>10000</pot_max> > >> >> >> >> >> > <!-- extend the tables to this value --> > >> >> >> >> >> > <table_end>2.5</table_end> > >> >> >> >> >> > > <initial_configuration>maindir</initial_configuration> > >> >> >> >> >> > <rdf> > >> >> >> >> >> > <block_length><DESC>Length of the block for the > >> >> >> >> >> > error > >> >> >> >> >> > analysis</DESC> > >> >> >> >> >> > 1000000 > >> >> >> >> >> > </block_length> > >> >> >> >> >> > <map><DESC>Special mapping file for rdf > calculations > >> >> >> >> >> > needed > >> >> >> >> >> > for > >> >> >> >> >> > bonded interactions</DESC> > >> >> >> >> >> > dopc_cg-map11.xml > >> >> >> >> >> > </map> > >> >> >> >> >> > <topol><DESC> Gromacs binary topol (tpr) file to > be > >> >> >> >> >> > used > >> >> >> >> >> > for > >> >> >> >> >> > csg_stat</DESC> > >> >> >> >> >> > topol-rdf.tpr > >> >> >> >> >> > </topol> > >> >> >> >> >> > <with_errors>yes<DESC>calculate error on the rdf: > >> >> >> >> >> > yes/no</DESC> > >> >> >> >> >> > </with_errors> > >> >> >> >> >> > </rdf> > >> >> >> >> >> > </gromacs> > >> >> >> >> >> > ----------- > >> >> >> >> >> > > >> >> >> >> >> > -- > >> >> >> >> >> > You received this message because you are subscribed to > the > >> >> >> >> >> > Google > >> >> >> >> >> > Groups > >> >> >> >> >> > "votca" group. > >> >> >> >> >> > To unsubscribe from this group and stop receiving emails > 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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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://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. 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