movie encode bug on Rocky Linux 8.4
Hello,
This time I am reporting what looks almost certainly like a bug.
Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log):
/usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for:
$ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6
If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root.
Thank you in advance,
Guillaume
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Hi Guillaume,
I made a bug report for this.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5314
Missing shared libraries on the various Linux distributions is a never ending scourge. Almost always I have seen links that include 1, 2, and 3 digit version suffixes. I think this is a deficiency of the RPM you got. I would be very surprised if CentOS 8 or RHEL 8 fails to encode movies in ChimeraX as no one has reported that.
Could you reply to the bug report email whether you installed the ChimeraX generic linux build or ChimeraX RPM? I believe the generic Linux ChimeraX distribution is especially prone to missing libraries because it does not use a package manager.
Tom
On Sep 29, 2021, at 3:32 AM, Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
This time I am reporting what looks almost certainly like a bug.
Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log):
/usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for:
$ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6
If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root.
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you! I installed ChimeraX using the RPM package for CentOS/RHEL 8. I also posted this info in the bug report.
Guillaume
On 29 Sep 2021, at 22:28, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
I made a bug report for this.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5314
Missing shared libraries on the various Linux distributions is a never ending scourge. Almost always I have seen links that include 1, 2, and 3 digit version suffixes. I think this is a deficiency of the RPM you got. I would be very surprised if CentOS 8 or RHEL 8 fails to encode movies in ChimeraX as no one has reported that.
Could you reply to the bug report email whether you installed the ChimeraX generic linux build or ChimeraX RPM? I believe the generic Linux ChimeraX distribution is especially prone to missing libraries because it does not use a package manager.
Tom
On Sep 29, 2021, at 3:32 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello,
This time I am reporting what looks almost certainly like a bug.
Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log):
/usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for:
$ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6
If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root.
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
<chimerax-libbz2-error.txt>
I ran into this same problem a few times in both CentOS 7 and Fedora 24, both for ffmpeg and MatPlotLib (really bz2 in the latter case) (tickets #668 and #1165), but it's been masked for me ever since because I just added the missing libbz2.so.1.0->libbz2.so.1.0.6 symlink in /usr/lib64. Looking at a recent CentOS 7 daily build, it looks like it's still current (or has re-emerged):
ldd /usr/libexec/UCSF-ChimeraX-daily/bin/ffmpeg
linux-vdso.so.1 => (0x00007ffd75dcd000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f25cb849000) libm.so.6 => /lib64/libm.so.6 (0x00007f25cb547000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f25cb343000) liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f25cb11d000) libbz2.so.1.0 => /lib64/libbz2.so.1.0 (0x00007f25caf0d000) libz.so.1 => /lib64/libz.so.1 (0x00007f25cacf7000) libc.so.6 => /lib64/libc.so.6 (0x00007f25ca929000) /lib64/ld-linux-x86-64.so.2 (0x00007f25cba65000)
Can't check the bz2 example because the compiled _bz2 library is missing - which probably means that the yum bzip2 package isn't installed in the image used for compiling ChimeraX.
________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Guillaume Gaullier via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: 30 September 2021 12:04 To: goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] movie encode bug on Rocky Linux 8.4
Thank you! I installed ChimeraX using the RPM package for CentOS/RHEL 8. I also posted this info in the bug report.
Guillaume
On 29 Sep 2021, at 22:28, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
I made a bug report for this.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5314
Missing shared libraries on the various Linux distributions is a never ending scourge. Almost always I have seen links that include 1, 2, and 3 digit version suffixes. I think this is a deficiency of the RPM you got. I would be very surprised if CentOS 8 or RHEL 8 fails to encode movies in ChimeraX as no one has reported that.
Could you reply to the bug report email whether you installed the ChimeraX generic linux build or ChimeraX RPM? I believe the generic Linux ChimeraX distribution is especially prone to missing libraries because it does not use a package manager.
Tom
On Sep 29, 2021, at 3:32 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hello,
This time I am reporting what looks almost certainly like a bug.
Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log):
/usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for:
$ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6
If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root.
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<chimerax-libbz2-error.txt>
participants (3)
-
Guillaume Gaullier -
Tom Goddard -
Tristan Croll