Dear Sir/Madame, I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in /usr/local/bin/chimera, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly? Thank you very much for your attention, Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
Try running "chimera --debug" and CHIMERA/bin/linuxdist and sending me the output from both programs. That said, it's probably a problem with the graphics driver. If you have AMD or NVIDIA graphics, try installing the proprietary graphics driver -- the proprietary drivers are much faster than the open source ones. If you have Intel graphics, then the best way to get a better driver is to upgrade to a newer version of Ubuntu. If you have AMD graphics and it still doesn't work with the proprietary driver, then try the Chimera daily build (can't remember if that happened with Ubuntu 14.04, but it is a problem with 15.04 -- the open source AMD driver works in 15.04 but is slower than the proprietary AMD driver). HTH, Greg On 2/6/2016 2:41 PM, Quim Aguirre wrote:
Dear Sir/Madame,
I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in |/usr/local/bin/chimera|, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly?
Thank you very much for your attention,
Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com <mailto:quim.aguirre@gmail.com> joaquim.aguirre01@estudiant.upf.edu <mailto:joaquim.aguirre01@estudiant.upf.edu>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I installed Chimera on an old all-in-one iMac with AMD RV630/M76 [Mobility Radeon HD 2600/ 2700]. It worked fine under Ubuntu 12.04, but stubbornly stopped working after upgrading the OS. Eventually I gave up and went back to 12.04 with the "radeon" driver. It works smoothly at least for what I've needed so far. Michael ________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of Greg Couch [gregc@cgl.ucsf.edu] Sent: Sunday, February 07, 2016 04:21 To: Quim Aguirre; chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Chimera does not run Try running "chimera --debug" and CHIMERA/bin/linuxdist and sending me the output from both programs. That said, it's probably a problem with the graphics driver. If you have AMD or NVIDIA graphics, try installing the proprietary graphics driver -- the proprietary drivers are much faster than the open source ones. If you have Intel graphics, then the best way to get a better driver is to upgrade to a newer version of Ubuntu. If you have AMD graphics and it still doesn't work with the proprietary driver, then try the Chimera daily build (can't remember if that happened with Ubuntu 14.04, but it is a problem with 15.04 -- the open source AMD driver works in 15.04 but is slower than the proprietary AMD driver). HTH, Greg On 2/6/2016 2:41 PM, Quim Aguirre wrote: Dear Sir/Madame, I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in /usr/local/bin/chimera, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly? Thank you very much for your attention, Quim [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] -- Joaquim Aguirre Plans Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com<mailto:quim.aguirre@gmail.com> joaquim.aguirre01@estudiant.upf.edu<mailto:joaquim.aguirre01@estudiant.upf.edu> _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The output of *chimera --debug* is: initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: r600_dri.so libGL error: driver pointer missing libGL error: failed to load driver: r600 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1419 Current serial number in output stream: 1420 And the output of *CHIMERA/bin/linuxdist* is: /etc/debian_version: jessie/sid /etc/lsb-release: DISTRIB_ID=Ubuntu DISTRIB_RELEASE=14.04 DISTRIB_CODENAME=trusty DISTRIB_DESCRIPTION="Ubuntu 14.04.3 LTS" /etc/os-release: NAME="Ubuntu" VERSION="14.04.3 LTS, Trusty Tahr" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 14.04.3 LTS" VERSION_ID="14.04" HOME_URL="http://www.ubuntu.com/" SUPPORT_URL="http://help.ubuntu.com/" BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/" /proc/cpuinfo: cpu: 4 GenuineIntel Intel(R) Core(TM) i3 CPU M 370 @ 2.40GHz (x86_64) cpu MHz: 2399.000 cache: 3072 KB /proc/meminfo: MemTotal: 3908624 kB Graphics: 01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Park [Mobility Radeon HD 5430/5450/5470] Thank you very much for your help!! Quim 2016-02-07 9:38 GMT+01:00 Michael Elbaum <michael.elbaum@weizmann.ac.il>:
I installed Chimera on an old all-in-one iMac with AMD RV630/M76 [Mobility Radeon HD 2600/ 2700]. It worked fine under Ubuntu 12.04, but stubbornly stopped working after upgrading the OS. Eventually I gave up and went back to 12.04 with the "radeon" driver. It works smoothly at least for what I've needed so far. Michael
------------------------------ *From:* chimera-users-bounces@cgl.ucsf.edu [ chimera-users-bounces@cgl.ucsf.edu] on behalf of Greg Couch [ gregc@cgl.ucsf.edu] *Sent:* Sunday, February 07, 2016 04:21 *To:* Quim Aguirre; chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Chimera does not run
Try running "chimera --debug" and CHIMERA/bin/linuxdist and sending me the output from both programs. That said, it's probably a problem with the graphics driver. If you have AMD or NVIDIA graphics, try installing the proprietary graphics driver -- the proprietary drivers are much faster than the open source ones. If you have Intel graphics, then the best way to get a better driver is to upgrade to a newer version of Ubuntu. If you have AMD graphics and it still doesn't work with the proprietary driver, then try the Chimera daily build (can't remember if that happened with Ubuntu 14.04, but it is a problem with 15.04 -- the open source AMD driver works in 15.04 but is slower than the proprietary AMD driver).
HTH,
Greg
On 2/6/2016 2:41 PM, Quim Aguirre wrote:
Dear Sir/Madame,
I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in /usr/local/bin/chimera, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly?
Thank you very much for your attention,
Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
_______________________________________________ Chimera-users mailing listChimera-users@cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
This confirms that the bug with the graphics driver. Start the "Software & Updates" tool in "System Settings", then switch to the "Additional Drivers" tab, and wait, and wait, and wait until it gives you a bunch of choices. Then choose "Using Video driver for the AMD graphics accelerators from fglrx (proprietary)", and click the "Apply Changes" button. And then reboot your computer and try Chimera again. For a simple test, install the mesa-utils package and run the glxgears program instead of Chimera. HTH, Greg On 02/07/2016 06:00 AM, Quim Aguirre wrote:
The output of *chimera --debug* is:
initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: r600_dri.so libGL error: driver pointer missing libGL error: failed to load driver: r600 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1419 Current serial number in output stream: 1420
And the output of *CHIMERA/bin/linuxdist* is:
/etc/debian_version: jessie/sid /etc/lsb-release: DISTRIB_ID=Ubuntu DISTRIB_RELEASE=14.04 DISTRIB_CODENAME=trusty DISTRIB_DESCRIPTION="Ubuntu 14.04.3 LTS" /etc/os-release: NAME="Ubuntu" VERSION="14.04.3 LTS, Trusty Tahr" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 14.04.3 LTS" VERSION_ID="14.04" HOME_URL="http://www.ubuntu.com/" SUPPORT_URL="http://help.ubuntu.com/" BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
/proc/cpuinfo: cpu: 4 GenuineIntel Intel(R) Core(TM) i3 CPU M 370 @ 2.40GHz (x86_64) cpu MHz: 2399.000 cache: 3072 KB
/proc/meminfo: MemTotal: 3908624 kB
Graphics: 01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Park [Mobility Radeon HD 5430/5450/5470]
Thank you very much for your help!!
Quim
2016-02-07 9:38 GMT+01:00 Michael Elbaum <michael.elbaum@weizmann.ac.il <mailto:michael.elbaum@weizmann.ac.il>>:
I installed Chimera on an old all-in-one iMac with AMD RV630/M76 [Mobility Radeon HD 2600/ 2700]. It worked fine under Ubuntu 12.04, but stubbornly stopped working after upgrading the OS. Eventually I gave up and went back to 12.04 with the "radeon" driver. It works smoothly at least for what I've needed so far. Michael
------------------------------------------------------------------------ *From:* chimera-users-bounces@cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu> [chimera-users-bounces@cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>] on behalf of Greg Couch [gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>] *Sent:* Sunday, February 07, 2016 04:21 *To:* Quim Aguirre; chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> *Subject:* Re: [Chimera-users] Chimera does not run
Try running "chimera --debug" and CHIMERA/bin/linuxdist and sending me the output from both programs. That said, it's probably a problem with the graphics driver. If you have AMD or NVIDIA graphics, try installing the proprietary graphics driver -- the proprietary drivers are much faster than the open source ones. If you have Intel graphics, then the best way to get a better driver is to upgrade to a newer version of Ubuntu. If you have AMD graphics and it still doesn't work with the proprietary driver, then try the Chimera daily build (can't remember if that happened with Ubuntu 14.04, but it is a problem with 15.04 -- the open source AMD driver works in 15.04 but is slower than the proprietary AMD driver).
HTH,
Greg
On 2/6/2016 2:41 PM, Quim Aguirre wrote:
Dear Sir/Madame,
I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in |/usr/local/bin/chimera|, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly?
Thank you very much for your attention,
Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 <tel:%2B34%20692%20352%20112> quim.aguirre@gmail.com <mailto:quim.aguirre@gmail.com> joaquim.aguirre01@estudiant.upf.edu <mailto:joaquim.aguirre01@estudiant.upf.edu>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com <mailto:quim.aguirre@gmail.com> joaquim.aguirre01@estudiant.upf.edu <mailto:joaquim.aguirre01@estudiant.upf.edu>
Wow, it works!!! Thank you very much Greg, and all the chimera users. You are an awesome team. Thanks for everything, Quim 2016-02-08 21:15 GMT+01:00 Greg Couch <gregc@cgl.ucsf.edu>:
This confirms that the bug with the graphics driver. Start the "Software & Updates" tool in "System Settings", then switch to the "Additional Drivers" tab, and wait, and wait, and wait until it gives you a bunch of choices. Then choose "Using Video driver for the AMD graphics accelerators from fglrx (proprietary)", and click the "Apply Changes" button. And then reboot your computer and try Chimera again.
For a simple test, install the mesa-utils package and run the glxgears program instead of Chimera.
HTH,
Greg
On 02/07/2016 06:00 AM, Quim Aguirre wrote:
The output of *chimera --debug* is:
initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: r600_dri.so libGL error: driver pointer missing libGL error: failed to load driver: r600 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1419 Current serial number in output stream: 1420
And the output of *CHIMERA/bin/linuxdist* is:
/etc/debian_version: jessie/sid /etc/lsb-release: DISTRIB_ID=Ubuntu DISTRIB_RELEASE=14.04 DISTRIB_CODENAME=trusty DISTRIB_DESCRIPTION="Ubuntu 14.04.3 LTS" /etc/os-release: NAME="Ubuntu" VERSION="14.04.3 LTS, Trusty Tahr" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 14.04.3 LTS" VERSION_ID="14.04" HOME_URL="http://www.ubuntu.com/" SUPPORT_URL="http://help.ubuntu.com/" BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
/proc/cpuinfo: cpu: 4 GenuineIntel Intel(R) Core(TM) i3 CPU M 370 @ 2.40GHz (x86_64) cpu MHz: 2399.000 cache: 3072 KB
/proc/meminfo: MemTotal: 3908624 kB
Graphics: 01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Park [Mobility Radeon HD 5430/5450/5470]
Thank you very much for your help!!
Quim
2016-02-07 9:38 GMT+01:00 Michael Elbaum <michael.elbaum@weizmann.ac.il>:
I installed Chimera on an old all-in-one iMac with AMD RV630/M76 [Mobility Radeon HD 2600/ 2700]. It worked fine under Ubuntu 12.04, but stubbornly stopped working after upgrading the OS. Eventually I gave up and went back to 12.04 with the "radeon" driver. It works smoothly at least for what I've needed so far. Michael
------------------------------ *From:* <chimera-users-bounces@cgl.ucsf.edu> chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of Greg Couch [gregc@cgl.ucsf.edu] *Sent:* Sunday, February 07, 2016 04:21 *To:* Quim Aguirre; <chimera-users@cgl.ucsf.edu> chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Chimera does not run
Try running "chimera --debug" and CHIMERA/bin/linuxdist and sending me the output from both programs. That said, it's probably a problem with the graphics driver. If you have AMD or NVIDIA graphics, try installing the proprietary graphics driver -- the proprietary drivers are much faster than the open source ones. If you have Intel graphics, then the best way to get a better driver is to upgrade to a newer version of Ubuntu. If you have AMD graphics and it still doesn't work with the proprietary driver, then try the Chimera daily build (can't remember if that happened with Ubuntu 14.04, but it is a problem with 15.04 -- the open source AMD driver works in 15.04 but is slower than the proprietary AMD driver).
HTH,
Greg
On 2/6/2016 2:41 PM, Quim Aguirre wrote:
Dear Sir/Madame,
I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in /usr/local/bin/chimera, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly?
Thank you very much for your attention,
Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 <%2B34%20692%20352%20112> quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
_______________________________________________ Chimera-users mailing listChimera-users@cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
-- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes quim.aguirre@gmail.com joaquim.aguirre01@estudiant.upf.edu
participants (3)
-
Greg Couch -
Michael Elbaum -
Quim Aguirre