Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix #31876

Mounium · 2017-11-20T22:34:07Z

Motivation for this change

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions
Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Fits CONTRIBUTING.md.

Mounium · 2017-11-21T11:16:03Z

Previous version of avogadro didn't build on current master (it said that libX11.so.6: No such file or directory even though ldd displayed a nix store entry), so I bumped it to a newer version. It uses eigen3_3.

Ma27 · 2017-11-22T08:25:54Z

pkgs/applications/science/chemistry/avogadro/default.nix

+  src = fetchFromGitHub {
+    owner = "cryos";
+    repo = "avogadro";
+    rev = "92e20f0072c51badd0849eb354b5cf4bfd05e6a3";


you can specify a tag as revision as well

Should I change it?

just personal taste, but pinning a package to a git tag explicitly shows me that this no random/unstable stuff from GitHub :-)

vbgl · 2017-12-03T09:21:36Z

pkgs/top-level/all-packages.nix

@@ -14250,9 +14244,6 @@ with pkgs;

  docker-machine = callPackage ../applications/networking/cluster/docker-machine { };
  docker-machine-kvm = callPackage ../applications/networking/cluster/docker-machine/kvm.nix { };
-  docker-machine-xhyve = callPackage ../applications/networking/cluster/docker-machine/xhyve.nix {


Why do you remove this? This seems unrelated to the other changes in this PR.

vbgl · 2017-12-03T09:27:30Z

pkgs/applications/science/chemistry/jmol/default.nix

+  };
+in
+stdenv.mkDerivation {
+  name = "jmol";


Please append a version number at the end of the name.

Mounium · 2017-12-04T19:00:42Z

pkgs/applications/science/chemistry/avogadro/default.nix

+  src = fetchFromGitHub {
+    owner = "cryos";
+    repo = "avogadro";
+    rev = "8ac8408ac6113d375cdcaf233f89854a23fa280c";


@Ma27 I used a non-tagged version here, because the tagged 1.2.0 one uses eigen 3.2, which is no longer packaged.

markuskowa · 2018-01-30T07:35:12Z

Building avogradro fails with build-use-sandbox enabled (cmake tries to download yaehmop):

-- Found Qt4: /nix/store/f2zybni1b4yy2hb8cz412i2242i46y5f-qt-4.8.7/bin/qmake (found suitable version "4.8.7", minimum required i 
CMake Warning (dev) at libavogadro/src/extensions/yaehmop/CMakeLists.txt:21:
  Syntax Warning in cmake code at column 29

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Downloading Yaehmop executable from https://github.com/psavery/yaehmop/releases/download/3.0.2/linux64-yaehmop.tgz
CMake Error at libavogadro/src/extensions/yaehmop/CMakeLists.txt:59 (file):
  file DOWNLOAD HASH mismatch

    for file: [/tmp/nix-build-avogadro-1.2.drv-0/source/build/bin/yaehmop.tgz]
      expected hash: [e878e96ea891d843ddb539b36da67117]
        actual hash: [d41d8cd98f00b204e9800998ecf8427e]
             status: [6;"Couldn't resolve host name"]



gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D3
-- Linking in static plugins: bsdyengine;navigatetool;elementcolor
contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_config_structure':
contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: warning: this 'if' clause does not guard... [-Wmisleading-indentat]
   if (NULL == fgets(fbuffer, 1024, data->file))
   ^~
contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:295:5: note: ...this statement, but the latter is misleadingly indented a'
     if (NULL == fgets(fbuffer, 1024, data->file))
     ^~
-- Found Doxygen: /nix/store/148n7shgrbfg0h6c0rmgdlsijixjdw4b-doxygen-1.8.11/bin/doxygen (found version "1.8.11") found component
g++ -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_FREET3
-- docbook tools not found, doc targets disabled
-- Configuring incomplete, errors occurred!
See also "/tmp/nix-build-avogadro-1.2.drv-0/source/build/CMakeFiles/CMakeOutput.log".
See also "/tmp/nix-build-avogadro-1.2.drv-0/source/build/CMakeFiles/CMakeError.log".
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D3
builder for ‘/nix/store/ak5giry0khs61x7dl1dwhfkvlm0qys46-avogadro-1.2.drv’ failed with exit code 1
error: build of ‘/nix/store/ak5giry0khs61x7dl1dwhfkvlm0qys46-avogadro-1.2.drv’ failed
The invocation of "nix-build -A jmol -A avogadro -A pymol /home/markus/.nox/nixpkgs" failed

Mounium · 2018-01-30T20:26:58Z

I didn't check it with sandbox yet, will have a look at it, but I can't do so currently.
Does it build without sandbox?

markuskowa · 2018-01-30T22:27:58Z

I can build it without sandboxing but the binary crashes with: "Invalid OpenGL context.
Either something is completely broken in your OpenGL setup (can you run any OpenGL application?), or you found a bug." (on mint linux/nix). I'll give it a try on NixOS later to check if I can run it there.

The problem with the sandbox is that a build process on nix should not download things. A better way to solve this would be to let nix download yaehmop and patch the cmake file to pick the version from the nix store (see e.g. https://github.com/NixOS/nixpkgs/blob/31637d09413c871b030c021eecf3abcee7c8b160/pkgs/applications/misc/nrsc5/default.nix).

markuskowa · 2018-01-31T05:07:53Z

When I try to run it on NixOS it segfaults without any further messages.

system: "x86_64-linux"
host os: Linux 4.9.78, NixOS, 17.09.2875.c2b668ee726 (Hummingbird)
multi-user?: no
sandbox: no
version: nix-env (Nix) 1.11.16

Mounium · 2018-01-31T10:46:22Z

It was quite a bit earlier that I made this pull request and it did build at the then current nixpkgs master. Also, I didn't remember it downloading something outside of nixpkgs, probably it didn't cause a problem then.

On non-nixos distros I believe that nothing works that need opengl without setting it up (nix doesn't link graphic libraries by default, it tries to find theme inside /run, this is the only non-pure part as far as I know, you can find an issue with a partial solution somewhere that uses the system libs with LD_LIBRARY_PATH, I think). As for the NixOS part, there definitely is some sort of problem, will try to repackage it, but can only do so tomorrow evening. Maybe try to change to a more recent revision of avogadro if you have the time/need it sooner. It's a tricky package, last time I tried it didn't even work on arch linux for some reason

markuskowa · 2018-01-31T17:24:07Z

Thanks for the OpenGL tip. I have tried avogadro 1.2.0, but the segfault problem on NixOS is the same.

Mounium · 2018-02-02T20:50:39Z

Strange thing is that it builds for me without trouble (although I didn't try with sandbox yet), and I can run it even on current master.. Did you fork this branch and built that, or did you just cherry-pick my commits? Maybe try the latter one once more, I really don't know what could be the problem..

GrahamcOfBorg added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Nov 20, 2017

Mounium force-pushed the chem branch from d246e0e to 5866f19 Compare November 21, 2017 11:12

Mounium changed the title ~~Chemistry-related commits, jmol init, bumped pymol and tidied up all-packages.nix~~ Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix Nov 21, 2017

Ma27 reviewed Nov 22, 2017

View reviewed changes

vbgl reviewed Dec 3, 2017

View reviewed changes

Mounium added 2 commits December 4, 2017 19:37

all-packages.nix: made new block CHEMISTRY

7837d83

pymol: 1.8.4 -> 1.8.6

a30a8b7

Mounium force-pushed the chem branch from 5866f19 to 0613eac Compare December 4, 2017 18:57

Mounium commented Dec 4, 2017

View reviewed changes

Mounium added 2 commits December 11, 2017 19:24

avogadro: 1.1.1 -> 1.2.0

8b07f74

jmol: init at 14.25.2

fe9892d

Mounium force-pushed the chem branch from 0613eac to fe9892d Compare December 11, 2017 18:25

FRidh mentioned this pull request Jan 29, 2018

package avogadro is broken #34307

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Mounium closed this Mar 26, 2018

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Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix #31876

Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix #31876

Mounium commented Nov 20, 2017

Mounium commented Nov 21, 2017

Ma27 Nov 22, 2017

Mounium Nov 27, 2017

Ma27 Nov 27, 2017

vbgl Dec 3, 2017

vbgl Dec 3, 2017

Mounium Dec 4, 2017

markuskowa commented Jan 30, 2018

Mounium commented Jan 30, 2018

markuskowa commented Jan 30, 2018

markuskowa commented Jan 31, 2018

Mounium commented Jan 31, 2018

markuskowa commented Jan 31, 2018

Mounium commented Feb 2, 2018

Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix #31876

Chemistry-related commits, jmol init, bumped pymol, avogadro and tidied up all-packages.nix #31876

Conversation

Mounium commented Nov 20, 2017

Motivation for this change

Things done

Mounium commented Nov 21, 2017

Ma27 Nov 22, 2017

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markuskowa commented Jan 30, 2018

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Mounium commented Feb 2, 2018