Re: ng4ex gsun01n fails with segmentation fault on gentoo x86

Mary, yes it fails when run from compiled sources and shows a plot (two plots on subsequent click) when run from binaries: http://pier.unirc.eu/cestino/snapshot.png With debugger turned on gdb sends an endless list reporting the same error: #0 0xb7cedcfa in sincos () from /home/pier/Programmi/WRF/bin/ncl #1 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #2 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #3 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #4 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #5 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl --- snip --- #4154 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #4155 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #4156 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl --- snip --- #12349 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #12350 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #12351 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl --- snip --- #27536 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #27537 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl #27538 0xb7cedd1e in sincos () from /home/pier/Programmi/WRF/bin/ncl etc. etc. Pier --- Ven 23/4/10, Mary Haley <haley_at_ucar.edu> ha scritto: > Da: Mary Haley <haley_at_ucar.edu> > Oggetto: Re: [ncl-install] ng4ex gsun01n fails with segmentation fault on gentoo x86 > A: "Pierpaolo Garofalo" <pier_carla_at_yahoo.it> > Data: Venerdì 23 Aprile 2010, 23:25 > Pier, > > This is from the compiled source code, right? You said when > you run  > it from binary, it works? > > We may have to run this through a debugger since I can't > reproduce  > the problem here. > > Perhaps if you do the compile again with the debugging > turned on, and  > then we can > do something like this: > >   ng4ex xy01n -n >   gdb ncl > > When the debug prompt comes up, type: > >    run xy01n.ncl > > At this point, it should seg fault, and now you can type: > >    where > > You can try all this now before you rebuild with debugging > turned on,  > just to see > if it gives you any useful information. > > --Mary > > On Apr 23, 2010, at 2:03 AM, Pierpaolo Garofalo wrote: > > > It fails with a segmentation fault: > > > > ng4ex xy01n xy02n -clean > > > > NCAR Graphics NCL Example <xy01n> > > > >   Copying xy01n.ncl > >   Copying xy01.res > > > > Running NCL... > >  Copyright (C) 1995-2010 - All Rights Reserved > >  University Corporation for Atmospheric Research > >  NCAR Command Language Version 5.2.0 > >  The use of this software is governed by a > License Agreement. > >  See http://www.ncl.ucar.edu/ for more > details. > > Segmentation fault > > > > ncl failed. > > > > Pier > > > > --- Gio 22/4/10, Mary Haley <haley_at_ucar.edu> > ha scritto: > > > >> Da: Mary Haley <haley_at_ucar.edu> > >> Oggetto: Re: [ncl-install] ng4ex gsun01n fails > with segmentation  > >> fault on gentoo x86 > >> A: "Pierpaolo Garofalo" <pier_carla_at_yahoo.it> > >> Data: Giovedì 22 Aprile 2010, 23:16 > >> And what happens when you type this: > >> > >>     ng4ex xy01n xy02n -clean > >> > >> You will need to click on any window that pops up > with your > >> left > >> mouse button. > >> > >> -Mary > >> > >> On Apr 21, 2010, at 1:28 AM, Pierpaolo Garofalo > wrote: > >> > >>> Yes, > >>> it shows a plot. Here is a snapshot: > >>> > >>> http://pier.unirc.eu/cestino/snapshot.png > >>> > >>> > >>> Pier > >>> > >>> --- Mar 20/4/10, Mary Haley <haley_at_ucar.edu> > >> ha scritto: > >>> > >>>> Da: Mary Haley <haley_at_ucar.edu> > >>>> Oggetto: Re: [ncl-install] ng4ex gsun01n > fails > >> with segmentation > >>>> fault on gentoo x86 > >>>> A: "Pierpaolo Garofalo" <pier_carla_at_yahoo.it> > >>>> Data: Martedì 20 Aprile 2010, 22:56 > >>>> > >>>> On Apr 20, 2010, at 9:21 AM, Pierpaolo > Garofalo > >> wrote: > >>>> > >>>>> Mary, > >>>>> I checked the command ctrans again > this time > >> clicking > >>>> on the empty > >>>>> black window. This is the error > message: > >>>>> > >>>>> ctrans -d X11 gsun02n.ncgm > >>>>> ctrans: FATAL - Premature end of > metafile > >>>>> NCAR Graphics Fortran  Example > >> <agex01> > >>>>> > >>>>> > >>>>> Instead the command: > >>>>> > >>>>> > >>>>> ncargex -w x11 agex01 -clean > >>>>> > >>>>> returned a white graph on a black > window. The > >> terminal > >>>> message this > >>>>> time was: > >>>>> > >>>>> NOTE: This example is being run > interactively > >> and can > >>>> only > >>>>>      >    be executed if you > >> have > >>>> X running and have your > >>>>>      >    DISPLAY > >> environment > >>>> variable set properly.  It will > >>>>>      >    create an X11 > >> window > >>>> that you must click on with your > >>>>>      >    mouse to advance > >> the > >>>> frame(s). > >>>>> > >>>>>     Copying > agex01.f > >>>>> > >>>>> Compiling and linking... > >>>>> gfortran -fPIC -fno-second-underscore > >> -fno-range-check > >>>> -O -o agex01 > >>>>> agex01.f > >> -L/home/pier/Programmi/WRF/SW/ncarg/lib > >>>> -L/usr/X11R6/lib - > >>>>> L/usr/lib/gcc/1-pc-1-gnu/4.3.4 > >>>> -L/home/pier/Programmi/WRF/lib - > >>>>> lncarg -lncarg_gks -lncarg_c -lX11 > -lXext > >>>>> > >>>> > >> > /usr/lib/gcc/i686-pc-linux-gnu/4.3.4/../../../../i686-pc-linux-gnu/ > >>>> > >>>>> bin/ld: warning: creating a DT_TEXTREL > in > >> object. > >>>>> > >>>>> Executing <agex01>... > >>>>> > >>>>>    agex01.. > >>>>> > >>>>> > >>>>> The window disappeared as soon as I > clicked on > >> it but > >>>> without any > >>>>> error message. > >>>> > >>>> Did it show an XY plot before it > >> disappeared?  If so, > >>>> then this is > >>>> the correct behavior. > >>>> > >>>> --Mary > >>>> > >>>>> > >>>>> Regards, > >>>>> Pier > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> --- Mar 20/4/10, Mary Haley <haley_at_ucar.edu> > >>>> ha scritto: > >>>>> > >>>>>> Da: Mary Haley <haley_at_ucar.edu> > >>>>>> Oggetto: Re: [ncl-install] ng4ex > gsun01n > >> fails > >>>> with segmentation > >>>>>> fault on gentoo x86 > >>>>>> A: "Pierpaolo Garofalo" <pier_carla_at_yahoo.it> > >>>>>> Data: Martedì 20 Aprile 2010, > 00:47 > >>>>>> Pier, > >>>>>> > >>>>>> Thanks for sending the files, > Everything > >> seems to > >>>> look > >>>>>> okay. > >>>>>> > >>>>>> Can you try a more simple example? > I need > >> to see > >>>> if this is > >>>>>> an issue with "ncl" or some > low-level > >> code. > >>>>>> > >>>>>> Try this: > >>>>>> > >>>>>> ncargex -w x11 agex01 -clean > >>>>>> > >>>>>> As for the libxxxx.so problems, > did you > >> try > >>>> downloading a > >>>>>> non-OPeNDAP-enabled binary? These > binaries > >> don't > >>>> have those > >>>>>> dependencies. > >>>>>> > >>>>>> For the NCGM test you did below: > when you > >> run > >>>> "ctrans -d > >>>>>> X11 file.ncgm", it will pop up a > window, > >> but you > >>>> may need to > >>>>>> click > >>>>>> on that window with your left > mouse button > >> to > >>>> advance the > >>>>>> frame and close it. > >>>>>> > >>>>>> > >>>>>> --Mary > >>>>>> > >>>>>> > >>>>>> On Apr 19, 2010, at 1:11 PM, > Pierpaolo > >> Garofalo > >>>> wrote: > >>>>>> > >>>>>>> Mary, > >>>>>>> thank you very much for your > prompt > >> reply. > >>>>>>> > >>>>>>> I tried and compiled both > 5.1.0 and > >> 5.2.0 but > >>>> the > >>>>>> graphic tests on gsunxxn files > always fail > >> with > >>>> the same > >>>>>> error message. > >>>>>>> > >>>>>>> Versions 5.1.0 and 5.2.0 from > binaries > >> work > >>>> well (so > >>>>>> you might be righteous asking why > I am > >> bothering > >>>> the mailing > >>>>>> list with the compiling from > source not > >> working > >>>> matter... > >>>>>> fact is that I started from the > source > >> code and I > >>>> am a bit > >>>>>> disappointed about this hitch) > with a > >> difference > >>>> though, > >>>>>> version 5.2.0 from binaries > complains > >> with > >>>> warning > >>>>>> messages: > >>>>>>> > >>>>>>> ncl: > /usr/lib/libcrypto.so.0.9.8: no > >> version > >>>>>> information available (required by > ncl) > >>>>>>> ncl: /usr/lib/libssl.so.0.9.8: > no > >> version > >>>> information > >>>>>> available (required by ncl) > >>>>>>> > >>>>>>> (I realized that when asking > the > >> script from a > >>>> tcl-tk > >>>>>> script which prevented its normal > running > >> on > >>>> account of the > >>>>>> above warnings. In order to get > the ncl > >> script to > >>>> do its job > >>>>>> I had to redirect the error output > to > >> /dev/null, > >>>> so that > >>>>>> this is not much of a hassle) > >>>>>>> > >>>>>>> The output of ldd returns: > >>>>>>> > >>>>>>> ldd $(which ncl) > >>>>>>> > /home/pier/Programmi/WRF/bin/ncl: > >>>>>> /usr/lib/libcrypto.so.0.9.8: no > version > >>>> information > >>>>>> available (required by > >>>> /home/pier/Programmi/WRF/bin/ncl) > >>>>>>> > /home/pier/Programmi/WRF/bin/ncl: > >>>>>> /usr/lib/libssl.so.0.9.8: no > version > >> information > >>>> available > >>>>>> (required by > >> /home/pier/Programmi/WRF/bin/ncl) > >>>>>>> > >>>> linux-gate.so.1 > >>>>>> =>  (0xffffe000) > >>>>>>> > >>>>>>      > libcrypto.so.0.9.8 > >> => > >>>>>> /usr/lib/libcrypto.so.0.9.8 > (0xb7e76000) > >>>>>>> > >>>> libssl.so.0.9.8 > >>>>>> => /usr/lib/libssl.so.0.9.8 > >> (0xb7e2d000) > >>>>>>> > >>    librt.so.1 > >>>> => > >>>>>> /lib/librt.so.1 (0xb7e24000) > >>>>>>> > >>    libX11.so.6 > >>>>>> => /usr/lib/libX11.so.6 > (0xb7d0d000) > >>>>>>> > >>>> libXext.so.6 > >>>>>> => /usr/lib/libXext.so.6 > (0xb7cfd000) > >>>>>>> > >>    libm.so.6 > >>>> => > >>>>>> /lib/libm.so.6 (0xb7cd6000) > >>>>>>> > >>    libdl.so.2 > >>>> => > >>>>>> /lib/libdl.so.2 (0xb7cd2000) > >>>>>>> > >>>> libstdc++.so.6 > >>>>>> => > >>>> > >> > /usr/lib/gcc/i686-pc-linux-gnu/4.3.4/libstdc++.so.6 > >>>>>> (0xb7be6000) > >>>>>>> > >>>> libgcc_s.so.1 > >>>>>> => > >>>> > >> > /usr/lib/gcc/i686-pc-linux-gnu/4.3.4/libgcc_s.so.1 > >>>>>> (0xb7bd8000) > >>>>>>> > >>    libc.so.6 > >>>> => > >>>>>> /lib/libc.so.6 (0xb7a94000) > >>>>>>> > >>>> libpthread.so.0 > >>>>>> => /lib/libpthread.so.0 > (0xb7a7a000) > >>>>>>> > >>    libz.so.1 > >>>> => > >>>>>> > /home/pier/Programmi/WRF/lib/libz.so.1 > >>>> (0xb7a65000) > >>>>>>> > >>>>>>      > /lib/ld-linux.so.2 > >> (0xb7fd9000) > >>>>>>> > >>    libxcb.so.1 > >>>>>> => /usr/lib/libxcb.so.1 > (0xb7a4a000) > >>>>>>> > >>    libXau.so.6 > >>>>>> => /usr/lib/libXau.so.6 > (0xb7a46000) > >>>>>>> > >>>> libXdmcp.so.6 > >>>>>> => /usr/lib/libXdmcp.so.6 > (0xb7a40000) > >>>>>>> > >>>>>>> > >>>>>>> I put make-output and LINUX > files > >> here: > >>>>>>> > >>>>>>> > >>>>>>> http://pier.unirc.eu/cestino/LINUX > >>>>>>> http://pier.unirc.eu/cestino/make-output.gz > >>>>>>> > >>>>>>> > >>>>>>> Regards, > >>>>>>> Pier > >>>>>>> > >>>>>>> > >>>>>> > >>>> > >> > ----------------------------------------------------------------- > >>>>>>> .../\ /\ > >>>>>>> ....0 0 > >>>>>>> ....=O= > >>>>>>> <  Pierp  > > >>>>>>> > >>>>>> > >>>> > >> > ----------------------------------------------------------------- > >>>>>>> Linux Gentoo Ker. 2.6.22/Ker. > 2.6.19.2 > >> RTAI > >>>> Vulcano > >>>>>>> Web: http://pier.unirc.eu > >>>>>>> msn: pier_port at hotmail dot > com > >>>>>>> irc: irc.unirc.eu #linux > >>>>>>> icq: 325474062 > >>>>>>> > >>>>>> > >>>> > >> > ----------------------------------------------------------------- > >>>>>>> "Absolutely nothing should be > >> concluded from > >>>> these > >>>>>> figures except that no conclusion > can be > >> drawn > >>>> from them." > >>>>>>> > >>>>>> > >>>> > >> > ----------------------------------------------------------------- > >>>>>>> > >>>>>>> > >>>>>>> --- Lun 19/4/10, Mary Haley > <haley_at_ucar.edu> > >>>>>> ha scritto: > >>>>>>> > >>>>>>>> Da: Mary Haley <haley_at_ucar.edu> > >>>>>>>> Oggetto: Re: [ncl-install] > ng4ex > >> gsun01n > >>>> fails > >>>>>> with segmentation fault on gentoo > x86 > >>>>>>>> A: "Pierpaolo Garofalo" > <pier_carla_at_yahoo.it> > >>>>>>>> Cc: ncl-install_at_ucar.edu > >>>>>>>> Data: Lunedì 19 Aprile > 2010, > >> 16:13 > >>>>>>>> Pier, > >>>>>>>> > >>>>>>>> You are running a rather > old > >> version of > >>>> NCL. > >>>>>> You > >>>>>>>> might want to consider > upgrading. > >>>>>>>> > >>>>>>>> Did you install NCL from > source > >> code or > >>>> from a > >>>>>> precompiled > >>>>>>>> binary? > >>>>>>>> > >>>>>>>> If you installed from > source code, > >> then > >>>> there > >>>>>> might be a > >>>>>>>> problem with the > configuration > >> setup. > >>>>>>>> > >>>>>>>> If you installed from a > binary, > >> then I > >>>> suggest > >>>>>> upgrading to > >>>>>>>> NCL 5.2.0: > >>>>>>>> > >>>>>>>> http://www.ncl.ucar.edu/Download/ > >>>>>>>> > >>>>>>>> If you installed from > source code, > >> I > >>>> still > >>>>>> recommend > >>>>>>>> upgrading, but we'll need > to > >> figure > >>>>>>>> out if your configuration > is > >>>> correct.  Can > >>>>>> you send me > >>>>>>>> the $NCARG/config/LINUX > file > >>>>>>>> you used, and your > "make-output" > >> file? > >>>>>>>> > >>>>>>>> --Mary > >>>>>>>> > >>>>>>>> On Apr 17, 2010, at 2:07 > AM, > >> Pierpaolo > >>>> Garofalo > >>>>>> wrote: > >>>>>>>> > >>>>>>>>> Hi all, > >>>>>>>>> I have managed to > successfully > >> compile > >>>> and > >>>>>> install ncl > >>>>>>>> on a couple of quad core > x86_64 > >> gentoo > >>>> machines. > >>>>>>>> Nevertheless there must > be > >> something wrong > >>>> when I > >>>>>> do the > >>>>>>>> same on a Macbook > Santarosa with > >> x86 > >>>> gentoo when > >>>>>> preparing > >>>>>>>> for wrf-3.2. > >>>>>>>>> > >>>>>>>>> I realize that ncl is > not > >> properly > >>>> working on > >>>>>> this > >>>>>>>> latter machine . > >>>>>>>>> > >>>>>>>>> I have just been using > it with > >> a very > >>>> simple > >>>>>> script > >>>>>>>> aimed to extract > de-staggered data > >> from > >>>> wrf-3.2 > >>>>>> wrfout > >>>>>>>> files. As a matter of fact > the > >> script > >>>> below does > >>>>>> its job > >>>>>>>> well: > >>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>> > >>>> > >> > ------------------------------------------------------------ > >>>>>>>>> load > >>>>>>>> > >>>>>> > >>>> > >> > "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl" > >>>>>>>>> load > >>>>>>>> > >>>>>> > >>>> > >> > "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRFUserARW.ncl" > >>>>>>>>> > >>>>>>>>> begin > >>>>>>>>> > >>>>>>>>>      >    a > >> = > >>>>>> addfile("wrfout.nc","r") > >>>>>>>>> > >>>>>>>>>      >    U > >> = > >>>>>>>> > wrf_user_getvar(a,"ua",-1) > >>>>>>>>> > >>>>>>>>> > >>>>  >    asciiwrite("U.tmp",U) > >>>>>>>>> > >>>>>>>>>      >    V > >> = > >>>>>>>> > wrf_user_getvar(a,"va",-1) > >>>>>>>>> > >>>>>>>>> > >>>>  >    asciiwrite("V.tmp",V) > >>>>>>>>> > >>>>>>>>> end > >>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>> > >>>> > >> > ------------------------------------------------------------ > >>>>>>>>> > >>>>>>>>> whereas the graphics > doesn't > >> seem to > >>>> work: > >>>>>>>>> > >>>>>>>>> ng4ex gsun01n > >>>>>>>>> > >>>>>>>>> gives a quick flash of > a white > >> window > >>>> opening > >>>>>> and > >>>>>>>> suddenly closing in less > than a > >> tick. > >>>>>>>>> > >>>>>>>>> I did the following > to > >> investigate: > >>>>>>>>> > >>>>>>>>> 1) ulimit -s > unlimited > >>>>>>>>> > >>>>>>>>> the white window > persisted for > >> several > >>>> seconds > >>>>>> before > >>>>>>>> closing and giving back > the same > >> error > >>>> message: > >>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>> > >>>> > >> > ------------------------------------------------------- > >>>>>>>>> ng4ex gsun01n > >>>>>>>>> > >>>>>>>>> NCAR Graphics NCL > Example > >>>> <gsun01n> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> This example was set > up to > >> display the > >>>> output > >>>>>> to an > >>>>>>>>> X11 window. > >>>>>>>>> > >>>>>>>>>    >    Copying > >>>> gsun01n.ncl > >>>>>>>>> > >>>>>>>>> Running NCL... > >>>>>>>>> Copyright (C) > 1995-2009 - All > >> Rights > >>>> Reserved > >>>>>>>>> University Corporation > for > >>>> Atmospheric > >>>>>> Research > >>>>>>>>> NCAR Command Language > Version > >> 5.1.0 > >>>>>>>>> The use of this > software is > >> governed > >>>> by a > >>>>>> License > >>>>>>>> Agreement. > >>>>>>>>> See http://www.ncl.ucar.edu/ for more > >>>>>> details. > >>>>>>>>> Segmentation fault > >>>>>>>>> > >>>>>>>>> ncl failed. > >>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>> > >>>> > >> > ------------------------------------------------------- > >>>>>>>>> > >>>>>>>>> 2) I altered > >> gsun01n.ncl > >>>> swapping X11 > >>>>>> with ncgm > >>>>>>>> but I got the same error > message > >> again. > >>>>>> gsun01n.ncgm was > >>>>>>>> created but > >>>>>>>>> > >>>>>>>>> ctrans -d X11 > gsun01n.ncgm > >>>>>>>>> > >>>>>>>>> showed a black empty > window > >> this > >>>> time. > >>>>>>>>> > >>>>>>>>> 3) In order to > investigate > >> further I > >>>> gave the > >>>>>>>> command: > >>>>>>>>> > >>>>>>>>> strace ng4ex gsun01n > >> &> > >>>> log.err > >>>>>>>>> > >>>>>>>>> whose output is > available > >> here: > >>>>>>>>> > >>>>>>>>> http://pier.unirc.eu/cestino/log.err > >>>>>>>>> > >>>>>>>>> 4) As a last resort I > tried to > >> switch > >>>> from > >>>>>> intel to > >>>>>>>> vesa xorg driver but that > too > >> didn't > >>>> avail. > >>>>>>>>> > >>>>>>>>> I would like to point > out > >> that: > >>>>>>>>> a) I am able to use > idt as > >> well as > >>>> ncview.; > >>>>>>>>> b) compilation was > performed > >> by using > >>>> gcc > >>>>>> 4.3.4 and > >>>>>>>> gfortran; > >>>>>>>>> c) Kernel is > gentoo-2.6.30. > >>>>>>>>> > >>>>>>>>> Any hint on how to > solve this > >> would > >>>> be > >>>>>> greatly > >>>>>>>> appreciated. > >>>>>>>>> Regards, > >>>>>>>>> Pier > >>>>>>>>> > >>>>>>>>> > >>>> > ------------------------------------------ > >>>>>>>>> Pierpaolo Garofalo > >>>>>>>>> Dipartimento di > Ingegneria > >> Energetica > >>>>>>>>> Università > Politecnica delle > >> Marche > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>> > >> _______________________________________________ > >>>>>>>>> ncl-install mailing > list > >>>>>>>>> List instructions, > subscriber > >>>> options, > >>>>>> unsubscribe: > >>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-install > >>>>>>>> > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>> > >>> > >>> > >> > >> > > > > > > > >
Received on Sat Apr 24 01:56:51 2010