Cannot open an existing project

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Wed, 04/25/2018 - 14:43

wxh180

Cannot open an existing project

Dear all,

I've encountered a problem with opening an existing project file. The error message is:

"Error: mode 32746 MRC files not currently supported

Aborted (core dumped)"

Could you help me figure out what the problem is? Let me know if you need more information from me.

Thanks,

Wei

Wed, 04/25/2018 - 14:46

timgrant

Hi Wei,

This means it is trying to open a file that doesn't exist. Have you deleted anything from your project directory?

Tim

Wed, 04/25/2018 - 15:01

(Reply to #2) #3

wxh180

Hi Tim,

This error first occurred when I created a refinement package and cisTEM quit unexpectedly before the refinement package was finished. When I tried to re-open the .db file for this project, it shows me this error.

How can this problem be fixed? Thanks!

Best,

Wei

Wed, 04/25/2018 - 16:16

timgrant

Hi Wei,

So you didn't delete / move any files?

It is quite hard to diagnose, because we're not sure what it is looking for. Can you post the results of the following two commands (you need to replace my_database.db, with the name of your database) :-

sqlite3 my_database.db "select * from refinement_package_assets;"

and :-

sqlite3 my_database.db "select * from refinement_list;"

Thanks!

Tim

Wed, 04/25/2018 - 16:37

(Reply to #4) #5

wxh180

Hi Tim,

Here are the outputs:

1|Refinement Package #0|/scratch/sample0425/Assets/ParticleStacks/particle_stack_0.mrc|432|C1|3000.0|190.0|1|0|-1|0

2|Refinement Package #1|/scratch/sample0425/Assets/ParticleStacks/particle_stack_1.mrc|432|C1|3000.0|380.0|1|0|-1|0

and

1|1|Random Parameters|1|1285066369|-1|116944|1|432|0.85|100.0

2|2|Random Parameters|1|1285124406|-1|95249|1|432|0.85|100.0

And under /scratch/sample0425/Assets/ParticleStacks/, there is also an incompleted particle_stack_2.mrc, which does not show up in this inquiry. And cisTEM aborted while this particle_stack_2.mrc file is creating.

Please let me know if you need more information from me.

Thanks,

Wei

Wed, 04/25/2018 - 17:12

timgrant

Hi Wei,

I think the refinement packages look ok, and that the error is probably somewhere else. In order to get the bottom of it, I need to have an idea of where in the source it is crashing. Can you download a debug version of the cisTEM gui from here :-

http://grigoriefflab.janelia.org/sites/default/files/timgrant_18-04-25_5...

unzip it with :-

gzip -d cisTEM_debug.gz

then run it in GDB :-

gdb ./cisTEM_debug

At this point you need to type "run". The gui should then run, and you should be able to open your project. When it crashes, please type "bt" in the window and post the output.

Thanks!

Tim

Thu, 04/26/2018 - 16:04

(Reply to #6) #7

wxh180

Hi Tim,

Thanks! Unfortunately, I deleted the project and restarted one since cisTEM runs so fast.

But thanks again for this information. I will do this when I encountered this problem again.

Best,

Wei

Mon, 05/07/2018 - 19:46

wxh180

Hi Tim,

A similar problem happened again. This time it is in the generated 3D step. The job stopped so I terminated the job, then cisTEM crashed. And I can't open the project db file. Here is the output following your instructions running the debug version of cisTEM. Please let me know if you need more information from me. Thanks!

Best regards,

Wei

#######################

#0 0x00007ffff46401f7 in raise () from /usr/lib64/libc.so.6

#1 0x00007ffff46418e8 in abort () from /usr/lib64/libc.so.6

#2 0x0000000000912db9 in Database::ExecuteSQL (this=0x101ce, command=0x101ce <Address 0x101ce out of bounds>)

at core/database.cpp:36

#3 0x00000000008ed5c7 in Begin (this=<optimized out>) at core/database.h:31

#4 BeginCommitLocker (this=<optimized out>, wanted_database=<optimized out>) at core/database.cpp:2186

#5 Database::CreateAllTables (this=0x101ce) at core/database.cpp:658

#6 0x00000000008eced1 in Database::Open (this=0x101ce,

file_to_open=<error reading variable: Cannot access memory at address 0x101ce>, disable_locking=6)

at core/database.cpp:561

#7 0x0000000000920413 in Project::OpenProjectFromFile (this=0x101ce,

file_to_open=<error reading variable: Cannot access memory at address 0x101ce>) at core/project.cpp:151

#8 0x000000000053b2b3 in MyMainFrame::OpenProject (this=0x101ce,

project_filename=<error reading variable: Cannot access memory at address 0x101ce>) at gui/MainFrame.cpp:540

#9 0x000000000068961b in MyOverviewPanel::OnInfoURL (this=0x101ce, event=...) at gui/MyOverviewPanel.cpp:238

#10 0x0000000000e6126a in wxAppConsoleBase::HandleEvent(wxEvtHandler*, void (wxEvtHandler::*)(wxEvent&), wxEvent&) const ()

#11 0x0000000000e611c2 in wxAppConsoleBase::CallEventHandler(wxEvtHandler*, wxEventFunctor&, wxEvent&) const ()

#12 0x0000000000f76cc5 in wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) ()

#13 0x0000000000f76fb6 in wxEvtHandler::SearchDynamicEventTable(wxEvent&) ()

#14 0x0000000000f7784d in wxEvtHandler::TryHereOnly(wxEvent&) ()

#15 0x0000000000f78f87 in wxEvtHandler::TryBeforeAndHere(wxEvent&) ()

#16 0x0000000000f75f7f in wxEvtHandler::ProcessEventLocally(wxEvent&) ()

#17 0x0000000000f75d48 in wxEvtHandler::ProcessEvent(wxEvent&) ()

#18 0x0000000000db0ed1 in wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) ()

#19 0x0000000000a07b5e in wxRichTextCtrl::OnLeftUp(wxMouseEvent&) ()

#20 0x0000000000e6126a in wxAppConsoleBase::HandleEvent(wxEvtHandler*, void (wxEvtHandler::*)(wxEvent&), wxEvent&) const ()

#21 0x0000000000e611c2 in wxAppConsoleBase::CallEventHandler(wxEvtHandler*, wxEventFunctor&, wxEvent&) const ()

#22 0x0000000000f76cc5 in wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) ()

#23 0x0000000000f7505e in wxEventHashTable::HandleEvent(wxEvent&, wxEvtHandler*) ()

#24 0x0000000000f7789f in wxEvtHandler::TryHereOnly(wxEvent&) ()

#25 0x0000000000f78f87 in wxEvtHandler::TryBeforeAndHere(wxEvent&) ()

#26 0x0000000000f75f7f in wxEvtHandler::ProcessEventLocally(wxEvent&) ()

---Type <return> to continue, or q <return> to quit---

#27 0x0000000000f75d48 in wxEvtHandler::ProcessEvent(wxEvent&) ()

#28 0x0000000000db0ed1 in wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) ()

#29 0x0000000000f75e04 in wxEvtHandler::SafelyProcessEvent(wxEvent&) ()

#30 0x0000000000d5c5b5 in wxWindowBase::HandleWindowEvent(wxEvent&) const ()

#31 0x0000000000c11f7d in wxWindow::GTKProcessEvent(wxEvent&) const ()

#32 0x0000000000c0a84f in gtk_window_button_release_callback ()

#33 0x00007ffff789fbdc in _gtk_marshal_BOOLEAN__BOXED () from /usr/lib64/libgtk-x11-2.0.so.0

#34 0x00007ffff6387968 in g_closure_invoke () from /usr/lib64/libgobject-2.0.so.0

#35 0x00007ffff6399a7d in signal_emit_unlocked_R () from /usr/lib64/libgobject-2.0.so.0

#36 0x00007ffff63a17dc in g_signal_emit_valist () from /usr/lib64/libgobject-2.0.so.0

#37 0x00007ffff63a1ddf in g_signal_emit () from /usr/lib64/libgobject-2.0.so.0

#38 0x00007ffff79cfdc4 in gtk_widget_event_internal () from /usr/lib64/libgtk-x11-2.0.so.0

#39 0x00007ffff789de04 in gtk_propagate_event () from /usr/lib64/libgtk-x11-2.0.so.0

#40 0x00007ffff789e1fb in gtk_main_do_event () from /usr/lib64/libgtk-x11-2.0.so.0

#41 0x00007ffff74f8a0c in gdk_event_dispatch () from /usr/lib64/libgdk-x11-2.0.so.0

#42 0x00007ffff589e4c9 in g_main_context_dispatch () from /usr/lib64/libglib-2.0.so.0

#43 0x00007ffff589e818 in g_main_context_iterate.isra.21 () from /usr/lib64/libglib-2.0.so.0

#44 0x00007ffff589eaea in g_main_loop_run () from /usr/lib64/libglib-2.0.so.0

#45 0x00007ffff789d247 in gtk_main () from /usr/lib64/libgtk-x11-2.0.so.0

#46 0x0000000000de5da2 in wxGUIEventLoop::DoRun() ()

#47 0x0000000000e9f4c4 in wxEventLoopBase::Run (this=0x3730df0) at ./src/common/evtloopcmn.cpp:78

#48 0x0000000000e61db8 in wxAppConsoleBase::MainLoop() ()

#49 0x0000000000e60a6b in wxAppConsoleBase::OnRun() ()

#50 0x0000000000c8c6c9 in wxAppBase::OnRun() ()

#51 0x0000000000ed8ad8 in wxEntry(int&, wchar_t**) ()

#52 0x0000000000ed8bd0 in wxEntry(int&, char**) ()

#53 0x000000000043906d in main (argc=1, argv=0x101ce) at programs/projectx/projectx.cpp:14

Tue, 05/08/2018 - 12:04

(Reply to #8) #9

timgrant

Hi,

It looks like it's having trouble accessing the database file - is it possible you have run out of disk space?

Thanks,

Tim

Tue, 05/08/2018 - 13:34

(Reply to #9) #10

wxh180

Hi Tim,

You are right, just received the notification from our cluster admin saying that we are running out of quota.

It is the same "core dumped", but different error message from the previous one. I will let you know if I reproduced the previous error.

Thanks,

Wei

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Cannot open an existing project