Segmentation fault when issuing chimera command
Hi there, Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here. I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed. But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version. I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work. Any suggestions on how to deal with problem? Thanks a lot in advance! Hui
Hi Hui, Does Chimera crash if you start it without opening any data file? If that is the case then it is probably not the graphics driver, more likely some incompatible system library. If it crashes when you open a data file, what kind of data file is it (PDB, density map)? Tom
On Feb 28, 2017, at 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Thank you very much for your reply! I just type Chimera in the terminal window. I start it WITHOUT opening any data file. So, how can I figure out what causes the incompatibility issue? Thanks On Tue, Feb 28, 2017 at 6:10 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Hui,
Does Chimera crash if you start it without opening any data file? If that is the case then it is probably not the graphics driver, more likely some incompatible system library. If it crashes when you open a data file, what kind of data file is it (PDB, density map)?
Tom
On Feb 28, 2017, at 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
-- -------- Sincerely, Hui
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point. The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by. HTH, Greg On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Greg, Thank you for you reply! I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo command gave a very long list, for the first few lines, it gave this: name of display: :0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.4 Do you need the rest of the result? It is a really long one. I feel like it is better to keep it short in the mailing list. Hui On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point.
The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by.
HTH,
Greg
On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mail man/listinfo/chimera-users
-- -------- Sincerely, Hui
I am interested in the whole output. Not all of it is necessary -- I'm mostly interested in the lines that start with OpenGL and in the table at the end that describes the framebuffer configurations that are supported. It's easier to just send the whole thing. -- Greg On 2/28/2017 6:37 PM, Hui Shi wrote:
Hi Greg,
Thank you for you reply!
I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo command gave a very long list, for the first few lines, it gave this:
name of display: :0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.4
Do you need the rest of the result? It is a really long one. I feel like it is better to keep it short in the mailing list. Hui
On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point.
The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by.
HTH,
Greg
On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
-- -------- Sincerely, Hui
Hi Greg, Thanks again for your reply! I'm attaching a file of the glxinfo result here, named glxinfo_output. Hui On Tue, Feb 28, 2017 at 10:45 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
I am interested in the whole output. Not all of it is necessary -- I'm mostly interested in the lines that start with OpenGL and in the table at the end that describes the framebuffer configurations that are supported. It's easier to just send the whole thing.
-- Greg
On 2/28/2017 6:37 PM, Hui Shi wrote:
Hi Greg,
Thank you for you reply!
I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo command gave a very long list, for the first few lines, it gave this:
name of display: :0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.4
Do you need the rest of the result? It is a really long one. I feel like it is better to keep it short in the mailing list. Hui
On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point.
The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by.
HTH,
Greg
On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mail man/listinfo/chimera-users
-- -------- Sincerely, Hui
-- -------- Sincerely, Hui
The glxinfo output looks good. I'll work with you off the mailing list on this. -- Greg On 2/28/2017 11:07 PM, Hui Shi wrote:
Hi Greg,
Thanks again for your reply! I'm attaching a file of the glxinfo result here, named glxinfo_output. Hui
On Tue, Feb 28, 2017 at 10:45 PM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
I am interested in the whole output. Not all of it is necessary -- I'm mostly interested in the lines that start with OpenGL and in the table at the end that describes the framebuffer configurations that are supported. It's easier to just send the whole thing.
-- Greg
On 2/28/2017 6:37 PM, Hui Shi wrote:
Hi Greg,
Thank you for you reply!
I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo command gave a very long list, for the first few lines, it gave this:
name of display: :0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.4
Do you need the rest of the result? It is a really long one. I feel like it is better to keep it short in the mailing list. Hui
On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point.
The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by.
HTH,
Greg
On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
-- -------- Sincerely, Hui
-- -------- Sincerely, Hui
Turns out the problem was trying to run the 32-bit version of chimera on a system where only the 64-bit OpenGL setup was completely installed. Switching to the 64-bit version of chimera solved the problem. -- Greg On 3/1/2017 8:19 AM, Greg Couch wrote:
The glxinfo output looks good. I'll work with you off the mailing list on this.
-- Greg
On 2/28/2017 11:07 PM, Hui Shi wrote:
Hi Greg,
Thanks again for your reply! I'm attaching a file of the glxinfo result here, named glxinfo_output. Hui
On Tue, Feb 28, 2017 at 10:45 PM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
I am interested in the whole output. Not all of it is necessary -- I'm mostly interested in the lines that start with OpenGL and in the table at the end that describes the framebuffer configurations that are supported. It's easier to just send the whole thing.
-- Greg
On 2/28/2017 6:37 PM, Hui Shi wrote:
Hi Greg,
Thank you for you reply!
I have glx-utils-8.2.0-3.el7.x86_64 installed. And the glxinfo command gave a very long list, for the first few lines, it gave this:
name of display: :0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: NVIDIA Corporation server glx version string: 1.4
Do you need the rest of the result? It is a really long one. I feel like it is better to keep it short in the mailing list. Hui
On Tue, Feb 28, 2017 at 6:26 PM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
Most reported chimera bugs are due to faulty graphics drivers. So that is a good starting point.
The first thing to try is to confirm that the graphics driver is installed properly. If you don't have the glxinfo program installed yet, install the glx-utils package. Then run glxinfo and send me the output. If it fails to run, then you need to fix the graphics driver installation. It it succeeds, then I'll have something to go by.
HTH,
Greg
On 2/28/2017 4:55 PM, Hui Shi wrote:
Hi there,
Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here.
I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed.
But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version.
I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work.
Any suggestions on how to deal with problem? Thanks a lot in advance!
Hui _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
-- -------- Sincerely, Hui
-- -------- Sincerely, Hui
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Greg Couch -
Hui Shi -
Tom Goddard