Dear SPM experts,
we have problems to launch spm fmri.
SPM starts the initilization but never finishes and the terminal
provides the error message attached.
When using the debugging mode for spm.m the process stops at line 352
("spm_help(' !Disp' , url ...")
The initilization succedes with line 352 uncommented.
We used spm12 last modified $Date: 2020/01/14 10:51:47
I am not sure whether this is a local problem with my enviornment. I
installed spm12 under ubuntu 18.04.3 LTS with Matlab R2019.b.
Any help is welcom.
Best,
Nicole
--
Dr. Nicole Neef
Wissenschaftliche Mitarbeiterin
Klinik für Klinische Neurophysiologie
Universitätsmedizin Göttingen
Robert-Koch-Straße 40, 37075 Göttingen
Tel. +49 551 39 8461
user@computer:~/matlab$ The program 'MATLAB' received an X Window System error.
This probably reflects a bug in the program.
The error was 'RenderBadPicture (invalid Picture parameter)'.
(Details: serial 140957 error_code 143 request_code 139 minor_code 7)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)
MATLAB: management.cpp:712: find: Assertion `find: no active context for type 'mcos::COSContexI_Proxy'' failed.
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:23:02 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
com.mathworks.webservices.client.core.MathWorksClientException: unable to connect to host Connection refused (Connection refused)
at com.mathworks.webservices.client.core.MathWorksWebServiceClient.executeRequest(MathWorksWebServiceClient.java:308)
at com.mathworks.webservices.udc.client.UDCClientImpl.logEvents(UDCClientImpl.java:48)
at com.mathworks.fatalexit.FatalExitFrame.SendUDCMessage(FatalExitFrame.java:1100)
at com.mathworks.fatalexit.FatalExitFrame.sendCrashEvent(FatalExitFrame.java:1393)
at com.mathworks.fatalexit.FatalExitFrame.sendCrashEvent(FatalExitFrame.java:1424)
at com.mathworks.fatalexit.FatalExitFrame$13.run(FatalExitFrame.java:1294)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:666)
at sun.security.ssl.SSLSocketImpl.<init>(SSLSocketImpl.java:471)
at sun.security.ssl.SSLSocketFactoryImpl.createSocket(SSLSocketFactoryImpl.java:153)
at com.mathworks.webservices.client.core.http.HttpsProtocolSocketFactory.createSocket(HttpsProtocolSocketFactory.java:55)
at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
at com.mathworks.webservices.client.core.http.MathWorksHttpClient.invoke(MathWorksHttpClient.java:158)
at com.mathworks.webservices.client.core.MathWorksWebServiceClient.executeRequest(MathWorksWebServiceClient.java:214)
... 19 more
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: I/O exception (java.net.ConnectException) caught when processing request: Connection refused (Connection refused)
Jan 21, 2020 3:24:34 PM org.apache.commons.httpclient.HttpMethodDirector executeWithRetry
INFO: Retrying request
com.mathworks.webservices.client.core.MathWorksClientException: unable to connect to host Connection refused (Connection refused)
at com.mathworks.webservices.client.core.MathWorksWebServiceClient.executeRequest(MathWorksWebServiceClient.java:308)
at com.mathworks.webservices.udc.client.UDCClientImpl.logEvents(UDCClientImpl.java:48)
at com.mathworks.fatalexit.FatalExitFrame.SendUDCMessage(FatalExitFrame.java:1100)
at com.mathworks.fatalexit.FatalExitFrame.SendUDCMessage(FatalExitFrame.java:1109)
at com.mathworks.fatalexit.FatalExitFrame.sendCrashReport(FatalExitFrame.java:432)
at com.mathworks.fatalexit.FatalExitFrame$3.reportFile(FatalExitFrame.java:397)
at com.mathworks.fatalexit.SendReportPanel.show(SendReportPanel.java:131)
at com.mathworks.fatalexit.FatalExitFrame$10.actionPerformed(FatalExitFrame.java:763)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:666)
at sun.security.ssl.SSLSocketImpl.<init>(SSLSocketImpl.java:471)
at sun.security.ssl.SSLSocketFactoryImpl.createSocket(SSLSocketFactoryImpl.java:153)
at com.mathworks.webservices.client.core.http.HttpsProtocolSocketFactory.createSocket(HttpsProtocolSocketFactory.java:55)
at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
at com.mathworks.webservices.client.core.http.MathWorksHttpClient.invoke(MathWorksHttpClient.java:158)
at com.mathworks.webservices.client.core.MathWorksWebServiceClient.executeRequest(MathWorksWebServiceClient.java:214)
... 44 more
--------------------------------------------------------------------------------
Assertion detected at Di Jan 21 15:23:01 2020 +0100
--------------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : UTF-8
Deployed : false
Desktop Environment : ubuntu:GNOME
GNU C Library : 2.27 stable
Graphics Driver : Unknown hardware
Graphics card 1 : 0x10de ( 0x10de ) 0x1cb3 Version 410.78.0.0 (0-0-0)
Java Version : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
MATLAB Architecture : glnxa64
MATLAB Entitlement ID : 6704054
MATLAB Root : /usr/local/MATLAB/R2019b
MATLAB Version : 9.7.0.1216025 (R2019b) Update 1
OpenGL : hardware
Operating System : Ubuntu 18.04.3 LTS
Process ID : 1950
Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel
Session Key : f49044cb-0789-4237-9cab-e5a730b5d46a
Static TLS mitigation : Enabled: Full
Window System : The X.Org Foundation (11906000), display :1
Fault Count: 1
Assertion in find at management.cpp line 712:
find: no active context for type 'mcos::COSContexI_Proxy'
Register State (captured):
RAX = 00007f2bd825a878 RBX = 00007f2bd502ad08
RCX = 000000000000000a RDX = 00007f2bd501be00
RSP = 00007f2ac26df500 RBP = 00007f2ac26df8c0
RSI = 00007f2bd4fe32e6 RDI = 00007f2ac26df510
R8 = 00007f2ac26df7d5 R9 = 00007f2ac26df7d5
R10 = 0000000000000000 R11 = 00007f2ac26df650
R12 = 00007f2bd503ad98 R13 = 00007f2ac26e0160
R14 = 00007f2bd824fe8c R15 = 00007f2bd8250deb
RIP = 00007f2bd4f330be EFL = 0000000000000000
CS = e1ef FS = d81d GS = 7f2b
Stack Trace (captured):
[ 0] 0x00007f2bd4f2a623 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfl.so+00828963
[ 1] 0x00007f2bd4f2a81c /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfl.so+00829468 _ZN10foundation4core4diag15stacktrace_base7captureEm+00000028
[ 2] 0x00007f2bd4f2f44f /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfl.so+00848975
[ 3] 0x00007f2bd4f2f5b0 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfl.so+00849328
[ 4] 0x00007f2bd823f75e /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfoundation_usm.so+00075614
[ 5] 0x00007f2bd824c898 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwfoundation_usm.so+00129176 _ZN10foundation3usm6DetailINS0_5scope3MvmEE4findEmRKSt9type_info+00000136
[ 6] 0x00007f2bb8b8aa8a /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+02972298
[ 7] 0x00007f2bb8b896ad /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+02967213
[ 8] 0x00007f2bb8d6fd31 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+04959537
[ 9] 0x00007f2bce136cb9 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos.so+00273593 _ZN4mcos12COSInterface28getObjectBeingDestroyedEventEv+00000025
[ 10] 0x00007f2bb8baa1b4 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+03101108
[ 11] 0x00007f2bb8bab22a /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+03105322
[ 12] 0x00007f2bb8ba238c /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos_impl.so+03068812
[ 13] 0x00007f2bce137d05 /usr/local/MATLAB/R2019b/bin/glnxa64/libmwmcos.so+00277765 _ZN4mcos15COSInterfacePtrD1Ev+00000117
[ 14] 0x00007f2bc33a800f /usr/local/MATLAB/R2019b/bin/glnxa64/libmwm_interpreter.so+01085455 _ZN9MathWorks10MException18MExceptionEnvelopeD2Ev+00000079
[ 15] 0x00007f2bb9c3261d /usr/local/MATLAB/R2019b/bin/glnxa64/matlab_startup_plugins/matlab_graphics_ui/../../../../bin/glnxa64/libmwgui.so+00730653 _ZN9MCallbackD2Ev+00000189
[ 16] 0x00007f2bb9c32b31 /usr/local/MATLAB/R2019b/bin/glnxa64/matlab_startup_plugins/matlab_graphics_ui/../../../../bin/glnxa64/libmwgui.so+00731953 _ZN9MCallbackdlEPv+00000033
[ 17] 0x00007f2a955e960a /usr/local/MATLAB/R2019b/bin/glnxa64/builtins/matlab_graphics_hg/../../../../bin/glnxa64/libmwhg.so+04277770
[ 18] 0x00007f2a955f4088 /usr/local/MATLAB/R2019b/bin/glnxa64/builtins/matlab_graphics_hg/../../../../bin/glnxa64/libmwhg.so+04321416
[ 19] 0x00007f2a955e9a15 /usr/local/MATLAB/R2019b/bin/glnxa64/builtins/matlab_graphics_hg/../../../../bin/glnxa64/libmwhg.so+04278805
[ 20] 0x00007f2a955e9a81 /usr/local/MATLAB/R2019b/bin/glnxa64/builtins/matlab_graphics_hg/../../../../bin/glnxa64/libmwhg.so+04278913
[ 21] 0x00007f2a955f37a9 /usr/local/MATLAB/R2019b/bin/glnxa64/builtins/matlab_graphics_hg/../../../../bin/glnxa64/libmwhg.so+04319145
[ 22] 0x00007f2bd6a66041 /lib/x86_64-linux-gnu/libc.so.6+00274497
[ 23] 0x00007f2bd6a6613a /lib/x86_64-linux-gnu/libc.so.6+00274746
[ 24] 0x00007f2a848d3193 /usr/local/MATLAB/R2019b/bin/glnxa64/libgdk-x11-2.0.so.0+00401811
[ 25] 0x00007f2bc6d798fa /usr/lib/x86_64-linux-gnu/libX11.so.6+00264442 _XError+00000282
[ 26] 0x00007f2bc6d7682b /usr/lib/x86_64-linux-gnu/libX11.so.6+00251947
[ 27] 0x00007f2bc6d768d5 /usr/lib/x86_64-linux-gnu/libX11.so.6+00252117
[ 28] 0x00007f2bc6d77205 /usr/lib/x86_64-linux-gnu/libX11.so.6+00254469 _XEventsQueued+00000085
[ 29] 0x00007f2bc6d68cc0 /usr/lib/x86_64-linux-gnu/libX11.so.6+00195776 XEventsQueued+00000080
[ 30] 0x00007f2b35e1013e <unknown-module>+00000000
[ 31] 0x00007f2b35007d00 <unknown-module>+00000000
[ 32] 0x00007f2b350082bd <unknown-module>+00000000
[ 33] 0x00007f2b35008302 <unknown-module>+00000000
[ 34] 0x00007f2b350007a7 <unknown-module>+00000000
[ 35] 0x00007f2bb369f39b /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06849435
[ 36] 0x00007f2bb369cc63 /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06839395
[ 37] 0x00007f2bb369d227 /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06840871
[ 38] 0x00007f2bb370939c /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07283612
[ 39] 0x00007f2bb3a929eb /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+10992107
[ 40] 0x00007f2bb3a92cf1 /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+10992881
[ 41] 0x00007f2bb39248c2 /usr/local/MATLAB/R2019b/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+09492674
[ 42] 0x00007f2bd73b36db /lib/x86_64-linux-gnu/libpthread.so.0+00030427
[ 43] 0x00007f2bd6b4488f /lib/x86_64-linux-gnu/libc.so.6+01185935 clone+00000063
[ 44] 0x0000000000000000 <unknown-module>+00000000
** This crash report has been saved to disk as /home/user/matlab_crash_dump.1950-1 **
MATLAB is exiting because of fatal error
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