Re: ng4ex gsun01n fails with segmentation fault on gentoo x86

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 Fri Apr 23 02:10:46 2010