Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Thanks Paul for both messages. Thanks a ton for a summary of the various projects underway. I’m working on the build-it script on the Linux side while I figure out a ccp4 full license for my “self learning” small use. The build it script runs aground with some numpy libraries missing , even though I had python-numpy-dev..but i’ll keep at it. In the case of openssl missing errors..it was certainly installed and pointed to by the LD_LIBRARY_PATH..but it probably was a version mismatch because I had different version Hari On Wed, May 24, 2023 at 3:26 PM Paul Emsley wrote: > > On 24/05/2023 14:24, hari jayaram wrote: > > > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > *.-owner-c...@jiscmail.ac.uk-.* > > Hi All > I am making some progress--but still cant get any of the binaries working > > I have the openssl libraries installed but still get the following error > with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python > > Thanks for your help > Hari > > > > > "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ > ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > > > It is not clear to me if libcrypto is not installed (in which case you > should install it) or is a more modern version than my binary expects (in > which case, there is no hope for the binary that I have built (you might > like to try the build-it script)). > > Paul. > > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
On 24/05/2023 14:24, hari jayaram wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-c...@jiscmail.ac.uk-.* Hi All I am making some progress--but still cant get any of the binaries working I have the openssl libraries installed but still get the following error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python Thanks for your help Hari "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) It is not clear to me if libcrypto is not installed (in which case you should install it) or is a more modern version than my binary expects (in which case, there is no hope for the binary that I have built (you might like to try the build-it script)). Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
On 24/05/2023 02:13, hari jayaram wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-c...@jiscmail.ac.uk-.* Hi All I want to get back to using coot to build some models after a gap of 8 years. I have access to a Linux laptop and can put any OS version on it. I was wondering what the easiest way forward is —get the most recent Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso that coot was built for (20.04) on the laptop and start using it. The easiest way forward is to use the build from CCP4. They fiddle with it in minor annoying ways. It's robust. It comes with a lot of other stuff. You have to sign a license. Best way is to use the build-it script. Then you can track day-to-day development. The downside for this is that it often doesn't work out of the box. Having said that, all development tracking is a bit weird at the moment since there are 3 versions: - the 0.9.x series with old GTK and old python and old graphics - 1.0 the current release that depends on Gtk3 that doesn't work well on macOS - and maybe not Windows either - GTK4 Coot (which is another major rewrite). This is where I am spending my time (that and Moorhen). I want to get to a stage where GTK4 Coot is the only game in town. But there is a lot of work to do. And additional further work to make sure that it works well on macOS and Windows. What I can say about future Coots is that they will use your hardware - the more cores and better graphics card you have the more enjoyable/productive will be your Coot-using experience. Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground without OpenSSL and ldap.so versions are being mismatched. OpenSSL and Python are particularly time-consuming to correctly configure. I don't know how many days and weeks I've spend fiddling with it. Lots. Wretched thing. When I switched to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained of a version mismatch for libssl.so.1.1 I should make a Linux Mint virtual machine... Regards, Paul To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Hi All I am making some progress--but still cant get any of the binaries working I have the openssl libraries installed but still get the following error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python Thanks for your help Hari "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) . -- Coot crashed - trying to diagnose - ldd -r on guile gives: linux-vdso.so.1 (0x7ffdbdfae000) libguile.so.17 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libguile.so.17 (0x7f6d85ccc000) libc.so.6 (0x7f6d85aa4000) libgmp.so.10 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libgmp.so.10 (0x7f6d85a2b000) libcrypt.so.1 (0x7f6d859ef000) libm.so.6 (0x7f6d85908000) libltdl.so.3 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libltdl.so.3 (0x7f6d858fd000) libpthread.so.0 (0x7f6d858f8000) /lib64/ld-linux-x86-64.so.2 (0x7f6d85dd2000) libdl.so.2 (0x7f6d858f3000) Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: coot-exe: "/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin" /usr/bin/ls -rwxr-xr-x 1 hari hari 423402112 Mar 10 2022 /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin coot-version: /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) platform: /usr/bin/uname Linux LT-Hari-Linux 5.15.0-56-generic #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux core: #f No core file found. No debugging " On Tue, May 23, 2023 at 9:13 PM hari jayaram wrote: > Hi All > I want to get back to using coot to build some models after a gap of 8 > years. > > I have access to a Linux laptop and can put any OS version on it. > > I was wondering what the easiest way forward is —get the most recent > Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put > the iso that coot was built for (20.04) on the laptop and start using it. > > > Asking because I just tried using the newest mint distro ( Mint 21.1 > Vera) and one of the binaries > (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground > without OpenSSL and ldap.so versions are being mismatched. When I switched > to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it > complained of a version mismatch for libssl.so.1.1 > > Thanks for your help in advance > > > Hari > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
If you look through the coot archives there should be a thread where I asked about and showed some tips on autobuilding coot on a 20-or-so Ubuntu. The trickiest thing was apt installing anything coot stopped at, then just restart. I don't know the latest status of that whole process. -Bryan > On May 23, 2023, at 21:14, hari jayaram wrote: > > > Hi All > I want to get back to using coot to build some models after a gap of 8 years. > > I have access to a Linux laptop and can put any OS version on it. > > I was wondering what the easiest way forward is —get the most recent Ubuntu > and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso > that coot was built for (20.04) on the laptop and start using it. > > > Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) > and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) > and it runs aground without OpenSSL and ldap.so versions are being > mismatched. When I switched to > coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained > of a version mismatch for libssl.so.1.1 > > Thanks for your help in advance > > > Hari > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Hi All I want to get back to using coot to build some models after a gap of 8 years. I have access to a Linux laptop and can put any OS version on it. I was wondering what the easiest way forward is —get the most recent Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso that coot was built for (20.04) on the laptop and start using it. Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground without OpenSSL and ldap.so versions are being mismatched. When I switched to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained of a version mismatch for libssl.so.1.1 Thanks for your help in advance Hari To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
