[ncl-talk] problem with ncl_filedump *.nc ?
Rick Brownrigg
brownrig at ucar.edu
Tue Sep 18 20:24:21 MDT 2018
Hi Sam and Dylan,
I certainly appreciate both of you providing diagnostics in trying to
troubleshoot this matter. It pains me to say that: i) you even have to
experience this disruption, and ii) I can not replicate (and thus
troubleshoot) the problem in any fashion :-(
I could not glean any insight from the traces. A commonality seems to be
Ubuntu, so I stood up a fresh Ubuntu 18.02 distro (on a virtual machine),
and did a conda install of ncl into a fresh environment, and things work as
expected. Of note - in the minimalist installation of Ubuntu 18.02, I did
have to do an "apt-get" to install tcsh/csh -- do either of you recall this
being an issue for you, and how did you acquire your "C-shell"?
So, I don't get it -- ncl_filedump is nothing more than a C-shell script
that sets up a bunch of stuff and then calls NCL to do little more than (if
you were to do this from the command-line):
$ ncl
ncl 0> f = addfile("....your file...", "r")
ncl 1> print(f)
If either of you could//would, can you verify that at least this basic
functionality works?
I wish I had a better answer... :-/
Rick
On Mon, Sep 17, 2018 at 9:54 PM, Rick Brownrigg <brownrig at ucar.edu> wrote:
> Long story short -- Kevin and I have been talking about this issue with
> ncl_filedump, and another one he pointed out involving ng4ex. The
> commonalities are:
> - emerged in 6.5.0
> - both are c-shell drivers ultimately calling NCL
> - all known incidents occur on Ubuntu systems
>
> I engaged one of the users to provide me shell-traces and system-traces,
> but that was not revealing. He tells me that if he simply starts NCL and
> opens one of the problematic files with addfile(), everything is OK.
>
> I can't replicate the problems anywhere on systems I have access to, and
> am afraid we are going to have to stand up an Ubuntu syetem (VM) somewhere
> to try and replicate the issue, :-/
>
>
> ---------- Forwarded message ----------
> From: Sam McClatchie <smcclatchie at fishocean.info>
> Date: Mon, Sep 17, 2018 at 1:42 PM
> Subject: Re: [ncl-talk] problem with ncl_filedump *.nc ?
> To: Rick Brownrigg <brownrig at ucar.edu>
>
>
> Hello Rick
>
> Thanks for looking into this. I am using Ubuntu 18.04. Here is the output
> that you requested:
>
> smcc at jaguar:/data/dynamic_data/scratch$ ldd `which ncl`
> linux-vdso.so.1 (0x00007ffe281a0000)
> libssl.so.1.1 => /usr/lib/x86_64-linux-gnu/libssl.so.1.1
> (0x00007f2824005000)
> libcrypto.so.1.1 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.1
> (0x00007f2823b8d000)
> libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1
> (0x00007f2823983000)
> libfontconfig.so.1 => /usr/lib/x86_64-linux-gnu/libfontconfig.so.1
> (0x00007f282373e000)
> libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0
> (0x00007f282352e000)
> libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6
> (0x00007f28231f6000)
> libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6
> (0x00007f2822fe4000)
> libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
> (0x00007f2822cb3000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2822915000)
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2822711000)
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f2822383000)
> libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
> (0x00007f2822153000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f2821f3b000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f2821d1c000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f282192b000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f28278cb000)
> libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6
> (0x00007f2821677000)
> libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
> (0x00007f2821445000)
> libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1
> (0x00007f282121d000)
> libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
> (0x00007f2820fdd000)
> libpng16.so.16 => /usr/lib/x86_64-linux-gnu/libpng16.so.16
> (0x00007f2820dab000)
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2820b8e000)
> libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6
> (0x00007f282098a000)
> libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6
> (0x00007f2820784000)
> libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f282056f000)
> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f2820367000)
>
> smcc at jaguar:/data/dynamic_data/scratch$ uname -a
> Linux jaguar 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018
> x86_64 x86_64 x86_64 GNU/Linux
>
> smcc at jaguar:/data/dynamic_data/scratch$ gcc -v
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
> OFFLOAD_TARGET_NAMES=nvptx-none
> OFFLOAD_TARGET_DEFAULT=1
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> 7.3.0-16ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs
> --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr
> --with-gcc-major-version-only --with-as=/usr/bin/x86_64-linux-gnu-as
> --with-ld=/usr/bin/x86_64-linux-gnu-ld --program-suffix=-7
> --program-prefix=x86_64-linux-gnu- --enable-shared
> --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/
> --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes
> --with-default-libstdcxx-abi=new --enable-gnu-unique-object
> --disable-vtable-verify --enable-libmpx --enable-plugin
> --enable-default-pie --with-system-zlib --with-target-system-zlib
> --enable-objc-gc=auto --enable-multiarch --disable-werror
> --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32
> --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none
> --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu
> --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> Thread model: posix
> gcc version 7.3.0 (Ubuntu 7.3.0-16ubuntu3)
> smcc at jaguar:/data/dynamic_data/scratch$
>
> Best fishes
> Sam
>
> On 18/09/18 03:32, Rick Brownrigg wrote:
>
> This is odd -- I am able to dump all of these files, using my development
> version (which is still very 6.5.0-ish) and a bonafide 6.5.0 as installed
> via conda -- everything runs just fine.
>
> I wondering if I could get someone who is experiencing this issue to run:
>
> ldd `which ncl`
> uname -a
> gcc -v
>
> and send the output directly to me?
>
> Rick
>
>
> --
> Sam McClatchie (fisheries oceanographer)
> & Elena Turin (accounting & auditing)
> FishOcean Enterprises
> 38 Upland Rd, Huia, Auckland 0604, New Zealand
> <https://maps.google.com/?q=38+Upland+Rd,+Huia,+Auckland+0604,+New+Zealand&entry=gmail&source=g>
> cell: 027 752 8495
> Internet <http://www.fishocean.info>
>
>
> "The time has come", the tui said,
> "to talk of many things:
> Of songs - and ferns - and flowering flax,
> of Pukekos and dreams ..."
>
> (not Lewis Carroll)
>
>
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