Gephi can't initialize graph window

akamaus commented 1 year ago

Describe the bug

I tried several versions of gephi from nixos-20.03, nixos-21.11 and current master(1c8216d074). All have the same fatal issue: window stuck with 'initializing...' caption and no graph is displayed.

Steps To Reproduce

Steps to reproduce the behavior:

Install gephi
Load example graph
Observe no drawing is shown.

Additional context

I found precisely the same issue upstream. https://github.com/gephi/gephi/issues/2189 Both proposed solutions (setting either MESA_LOADER_DRIVER_OVERRIDE=i965 or LIBGL_ALWAYS_SOFTWARE=1) work for me.

Notify maintainers

@Radvendii

Metadata

% nix-shell -p nix-info --run "nix-info -m"                                                                                                                                                                         ~/nixpkgs 
 - system: `"x86_64-linux"`
 - host os: `Linux 5.10.102, NixOS, 21.11 (Porcupine)`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.3.16`
 - nixpkgs: `/opt/nixpkgs`

% glxinfo
name of display: :1
display: :1  screen: 0
direct rendering: Yes
server glx vendor string: SGI
server glx version string: 1.4
server glx extensions:
    GLX_ARB_create_context, GLX_ARB_create_context_no_error, 
    GLX_ARB_create_context_profile, GLX_ARB_create_context_robustness, 
    GLX_ARB_fbconfig_float, GLX_ARB_framebuffer_sRGB, GLX_ARB_multisample, 
    GLX_EXT_create_context_es2_profile, GLX_EXT_create_context_es_profile, 
    GLX_EXT_fbconfig_packed_float, GLX_EXT_framebuffer_sRGB, 
    GLX_EXT_import_context, GLX_EXT_libglvnd, GLX_EXT_no_config_context, 
    GLX_EXT_texture_from_pixmap, GLX_EXT_visual_info, GLX_EXT_visual_rating, 
    GLX_INTEL_swap_event, GLX_MESA_copy_sub_buffer, GLX_OML_swap_method, 
    GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, 
    GLX_SGIX_visual_select_group, GLX_SGI_make_current_read, 
    GLX_SGI_swap_control
...

% lspci | grep -i vga                                                                                                                                                                                               
00:02.0 VGA compatible controller: Intel Corporation CometLake-U GT2 [UHD Graphics] (rev 02)

importantblimp commented 1 year ago

Good news: this has been fixed on master since April, under commit ae5b53747bc06f479f1cf8164c7cadb1ee291d92. I haven't been able to tell which commit on master/staging/staging-next originally fixed the issue though.

Alizter commented 4 months ago

Any fix for this? None of the fixes in the gephi issue worked for me. I get

/nix/store/4w42z3xzhsr0zxqy9w3mag42n73n1xwz-dconf-0.40.0-lib/lib/gio/modules/libdconfsettings.so: undefined symbol: g_assertion_message_cmpint
Failed to load module: /nix/store/4w42z3xzhsr0zxqy9w3mag42n73n1xwz-dconf-0.40.0-lib/lib/gio/modules/libdconfsettings.so
/nix/store/9la894yvmmksqlapd4v16wvxpaw3rg70-glibc-2.37-8/lib/libc.so.6: version `GLIBC_2.38' not found (required by /nix/store/iv9bfnnnycgpsbsx4k9ncn6dpwrmrmmm-gvfs-1.52.2/lib/gio/modules/libgvfsdbus.so)
Failed to load module: /nix/store/iv9bfnnnycgpsbsx4k9ncn6dpwrmrmmm-gvfs-1.52.2/lib/gio/modules/libgvfsdbus.so
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.netbeans.core.windows.view.ui.MainWindow (jar:file:/nix/store/8l84g5g93djycc9402vnaw8av1dmwkp0-gephi-0.10.1/platform/modules/org-netbeans-core-windows.jar!/) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of org.netbeans.core.windows.view.ui.MainWindow
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

not really sure what to make of that.

MMesch commented 4 months ago

@importantblimp is this still working for you? After a brief phase where I was able to use gephi it stopped working again for me now. I also struggle to find a past commit that works, which makes me wonder whether a system driver update can influence this.

MMesch commented 4 months ago

Gephi shows, in the bottom right corner when clicking on a red street sign, this error message:

com.jogamp.opengl.GLException: Profile GL2 is not available on null, but: []

The export LIBGL_ALWAYS_SOFTWARE=1 doesn't have any effect but maybe I am not using it right.

MMesch commented 4 months ago

Workaround by @ErinvanderVeen :

Download the latest release here: https://github.com/gephi/gephi/releases/tag/v0.10.1 Extract it.

cd gephi-0.10.1-linux-x64/gephi-0.10.1/bin
NIXPKGS_ALLOW_UNFREE=1 nix run nixpkgs#steam-run --impure -- ./gephi

works for me and another colleague confirmed as well :+1:

ErinvanderVeen commented 4 months ago

Or, less hacky, use nixGL:

nix shell nixpkgs#gephi
nix run github:nix-community/nixGL --impure -- gephi

importantblimp commented 4 months ago

@MMesch, I think you're right, it's something environmental.

The commit that was previously working for me and the current version of unstable don't work for me now, although with a slightly different warning to Alizter. I see same behaviour as akamaus on the earlier commit, and a blank graph area with the latest unstable.

Outputs: Previously working for me (https://github.com/NixOS/nixpkgs/commit/ae5b53747bc06f479f1cf8164c7cadb1ee291d92):

/nix/store/ri1mxak4lk2k3l6zyb228ck354awlv2z-gephi-0.9.6
Detected KDE; adding awt.useSystemAAFontSettings=on
WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.netbeans.TopSecurityManager (file:/nix/store/ri1mxak4lk2k3l6zyb228ck354awlv2z-gephi-0.9.6/platform/lib/boot.jar)
WARNING: Please consider reporting this to the maintainers of org.netbeans.TopSecurityManager
WARNING: System::setSecurityManager will be removed in a future release

Latest unstable (fb96cbf93f08):

/nix/store/g06l7i9kl06aw8kf042478psvi49rmvq-gephi-0.10.1
Detected KDE; adding awt.useSystemAAFontSettings=on
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.netbeans.core.windows.view.ui.MainWindow (jar:file:/home/gy/src/nixpkgs/result/platform/modules/org-netbeans-core-windows.jar!/) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of org.netbeans.core.windows.view.ui.MainWindow
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

NixOS / nixpkgs