Gephi crashes when trying to open a graph on linux

[GaelMagnan]

Hi, i was trying out the nightly build on linux since we can't use the stable version du to it not working on java 8. I was using the oracle java version 8 an I encountered the following error:

hs_err_pid17292.txt

Gtk-Message: Failed to load module "canberra-gtk-module"
Current Version is 09-SNAPSHOT
Report created at /tmp/tempreport544250600915518157089386322184941
Report created at /tmp/tempreport787567999353505169289386322570257
Report created at /tmp/tempreport677202295196896003989386994707139
DATABRIDGE:
 Removed Edges: 0
 Added Edges: 0
 Removed Nodes: 0
 Added Nodes: 0
DATABRIDGE:
 Removed Edges: 0
 Added Edges: 1
 Removed Nodes: 0
 Added Nodes: 21101
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fec32f9f35c, pid=17292, tid=140652100069120
#
# JRE version: Java(TM) SE Runtime Environment (8.0_65-b17) (build 1.8.0_65-b17)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.65-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [i965_dri.so+0x1fa35c]
#
# Core dump written. Default location: /home/gael/workspace/core or core.17292
#
# An error report file with more information is saved as:
# /home/gael/workspace/hs_err_pid17292.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
/home/gael/gephi-0.9-SNAPSHOT/bin/../platform/lib/nbexec : ligne 474 : 17292 Abandon                 (core dumped)"/usr/lib/jvm/jre-8-oracle-x64/bin/java" -Djdk.home="/usr/lib/jvm/jre-8-oracle-x64" -classpath "/home/gael/gephi-0.9-SNAPSHOT/platform/lib/boot.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/org-openide-modules.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/org-openide-util.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/org-openide-util-lookup.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/org-openide-util-ui.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ar_SA.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_bg.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ca.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_cs.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_de.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_es.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_fr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_gl_ES.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_in_ID.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_it.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ja.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ko.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_nl_NL.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_pl.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_pt_BR.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_pt_PT.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ro.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_ru.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_si.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_sq.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_sv.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_tr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_zh_CN.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/boot_zh_TW.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ar_SA.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_bg.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ca.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_cs.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_de.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_es.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_fr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_gl_ES.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_in_ID.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_it.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ja.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ko.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_nl_NL.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_pl.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_pt_BR.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_pt_PT.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ro.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_ru.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_si.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_sq.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_sv.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_tr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_zh_CN.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-modules_zh_TW.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ar_SA.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_bg.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ca.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_cs.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_de.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_es.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_fr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_gl_ES.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_in_ID.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_it.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ja.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ko.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_bg.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_ca.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_cs.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_de.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_es.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_fr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_it.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_ja.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_ko.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_pl.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_ro.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_ru.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_si.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_sv.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_tr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_nl_NL.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_pl.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_pt_BR.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_pt_PT.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ro.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_ru.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_si.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_sq.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_sv.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_tr.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-ui_ja.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-ui_pt_BR.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-ui_ru.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util-ui_zh_CN.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_zh_CN.jar:/home/gael/gephi-0.9-SNAPSHOT/platform/lib/locale/org-openide-util_zh_TW.jar" -Dnetbeans.running.environment=gnome -Dnetbeans.dirs="/home/gael/gephi-0.9-SNAPSHOT/platform:/home/gael/gephi-0.9-SNAPSHOT/gephi:" -Dnetbeans.home="/home/gael/gephi-0.9-SNAPSHOT/platform" '-Xms512m' '-Xmx4g' '-Xverify:none' '-Dsun.java2d.noddraw=true' '-Dsun.awt.noerasebackground=true' '-Dnetbeans.indexing.noFileRefresh=true' '-Dplugin.manager.check.interval=EVERY_DAY' -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath="/home/gael/.gephi/0.9-SNAPSHOT/dev/var/log/heapdump.hprof" org.netbeans.Main --cachedir "/home/gael/.gephi/0.9-SNAPSHOT/dev/var/cache" --userdir "/home/gael/.gephi/0.9-SNAPSHOT/dev" "--branding" "gephi" 0<&0

It occured everytime I imported a graph, after the first analysis of the graph file.
Even with graphs as small as this one:

<?xml version='1.0' encoding='utf-8'?>
<gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
  <graph defaultedgetype="directed" mode="static">
    <nodes>
      <node id="1" label="1" />
      <node id="2" label="2" />
      <node id="3" label="3" />
      <node id="4" label="4" />
      <node id="5" label="5" />
      <node id="6" label="6" />
      <node id="7" label="7" />
      <node id="8" label="8" />
      <node id="9" label="9" />
    </nodes>
    <edges>
      <edge id="0" source="9" target="2" />
      <edge id="1" source="9" target="1" />
      <edge id="2" source="9" target="3" />
      <edge id="3" source="9" target="4" />
      <edge id="4" source="9" target="5" />
      <edge id="5" source="9" target="2" />
      <edge id="6" source="9" target="6" />
      <edge id="7" source="9" target="7" />
      <edge id="8" source="9" target="8" />
    </edges>
  </graph>
</gexf>

Hopes that helps.

[cybertib]

I think I have the same error.

When attempting to visualize a freshly created node, I obtain a crash on Gephi 0.8.2 and 0.9, both used with java-7-oracle.

Here is bug report.

thibault@thibault-UX303LB:~/Downloads/gephi-0.9.0/bin$ sh gephi --jdkhome /usr/lib/jvm/java-7-oracle/
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f1c04be40c6, pid=30471, tid=139758114076416
#
# JRE version: Java(TM) SE Runtime Environment (7.0_80-b15) (build 1.7.0_80-b15)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.80-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [i965_dri.so+0x1fb0c6]  _init+0x1c2f0e
#
# Core dump written. Default location: /home/thibault/Downloads/gephi-0.9.0/bin/core or core.30471
#
# An error report file with more information is saved as:
# /home/thibault/Downloads/gephi-0.9.0/bin/hs_err_pid30471.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
./../platform/lib/nbexec: line 474: 30471 Aborted                 (core dumped) "/usr/lib/jvm/java-7-oracle/bin/java" -Djdk.home="/usr/lib/jvm/java-7-oracle" -classpath "/home/thibault/Downloads/gephi-0.9.0/platform/lib/boot.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/org-openide-modules.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/org-openide-util.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/org-openide-util-lookup.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/org-openide-util-ui.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ar_SA.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_bg.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ca.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_cs.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_de.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_es.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_fr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_gl_ES.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_in_ID.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_it.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ja.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ko.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_nl_NL.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_pl.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_pt_BR.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_pt_PT.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ro.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_ru.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_si.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_sq.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_sv.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_tr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_zh_CN.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/boot_zh_TW.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ar_SA.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_bg.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ca.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_cs.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_de.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_es.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_fr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_gl_ES.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_in_ID.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_it.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ja.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ko.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_nl_NL.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_pl.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_pt_BR.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_pt_PT.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ro.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_ru.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_si.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_sq.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_sv.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_tr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_zh_CN.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-modules_zh_TW.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ar_SA.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_bg.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ca.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_cs.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_de.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_es.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_fr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_gl_ES.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_in_ID.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_it.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ja.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ko.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_bg.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_ca.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_cs.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_de.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_es.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_fr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_gl_ES.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_in_ID.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_it.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_ja.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_ko.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_nl_NL.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_pl.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_pt_BR.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_ro.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_ru.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_si.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_sv.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_tr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-lookup_zh_CN.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_nl_NL.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_pl.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_pt_BR.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_pt_PT.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ro.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_ru.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_si.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_sq.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_sv.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_tr.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-ui_ja.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-ui_pt_BR.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-ui_ru.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util-ui_zh_CN.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_zh_CN.jar:/home/thibault/Downloads/gephi-0.9.0/platform/lib/locale/org-openide-util_zh_TW.jar:/usr/lib/jvm/java-7-oracle/lib/dt.jar:/usr/lib/jvm/java-7-oracle/lib/tools.jar" -Dnetbeans.running.environment=gnome -Dnetbeans.dirs="/home/thibault/Downloads/gephi-0.9.0/platform:/home/thibault/Downloads/gephi-0.9.0/gephi:" -Dnetbeans.home="/home/thibault/Downloads/gephi-0.9.0/platform" '-Xms64m' '-Xmx512m' '-Xverify:none' '-Dsun.java2d.noddraw=true' '-Dsun.awt.noerasebackground=true' '-Dnetbeans.indexing.noFileRefresh=true' '-Dplugin.manager.check.interval=EVERY_DAY' -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath="/home/thibault/.gephi/0.9.0/dev/var/log/heapdump.hprof" org.netbeans.Main --cachedir "/home/thibault/.gephi/0.9.0/dev/var/cache" --userdir "/home/thibault/.gephi/0.9.0/dev" "--branding" "gephi" 0<&0

[robcat]

I have the same error with Archlinux, jdk8-openjdk, gephi 0.9.0 (both with sna and glamor).
This issue can be fixed on my system disabling the 3D acceleration, adding this line to the X configuration:

Option      "DRI"    "False"

After disabling DRI, gephi can open graphs correctly, but produces this message on startup:

libEGL warning: DRI2: failed to authenticate

[cschwem2er]

I have the same error with Linux Mint (x64).

[3ruce]

Running

LIBGL_ALWAYS_SOFTWARE=1 ./gephi

Did the trick for me with Intel drivers on xubuntu 14.04 - I found the workaround here. Another possible workaround was on launchpad but that didn't help.

[cschwem2er]

Thank you @3ruce for this tip. Can I set this line in some config file? I have no idea how Gephi works in the background.

[3ruce]

I guess it depends on how you run it - I just extracted the gephi archive and run it from my terminal using this..

cd ~/Downloads/gephi-0.9.0/bin LIBGL_ALWAYS_SOFTWARE=1 ./gephi

And it comes up working fine... If you've installed Gephi like a conventional ubuntu app and you've got an icon in a menu to click (I found some instructions for doing this via a PPA), you'll need to add the LIBGL line to the launcher/menu editor if that helps?

[cybertib]

This latest fix looks to work well for me. :) Many thanks !

Thibault

2016-02-03 10:20 GMT+01:00 Bruce notifications@github.com:

I guess it depends on how you run it - I just extracted the gephi archive
and run it from my terminal using this..

cd ~/Downloads/gephi-0.9.0/bin
LIBGL_ALWAYS_SOFTWARE=1 ./gephi

And it comes up working fine... If you've installed Gephi like a
conventional ubuntu app and you've got an icon in a menu to click (I found
some instructions for doing this via a PPA), you'll need to add the LIBGL
line to the launcher/menu editor if that helps?

—
Reply to this email directly or view it on GitHub
#1192 (comment).

[GaelMagnan]

Works for me too. Thanks.

[computermacgyver]

Thanks! I had the same trouble and adding the LIBGL_ALWAYS_SOFTWARE=1 option fixed it. To avoid typing this every time, I edited my etc/gephi.conf file and added the line

export LIBGL_ALWAYS_SOFTWARE=1

This way I can execute Gephi as normal via the terminal or desktop.

[rishidabre]

Thanks @3ruce and also @computermacgyver , Gephi 0.9.1 would crash on my Ubuntu 16.04.1 LTS as well, but it does not anymore after this fix.

[haydentech]

The "LIBGL_ALWAYS_SOFTWARE=1 ./gephi" workaround is still needed for me to successfully launch gephi on Ubuntu 16.04.3. It worked out of the box the first time I launched the program, but never again.