Hello, I just downloaded the latest coot (4322) and attempted to luanch on a new CentOS 6 machine. Coot was none too happy.
Here is the output. I'm not sure how to turn on debugging or core dumps, but if that would be useful I can redo this. classen@samos:/home/classen 1012% /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot COOT_PREFIX is /home/programs/coot-Linux-x86_64-centos-6-gtk2-python /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real Acquiring application resources from /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/share/coot/cootrc INFO:: splash_screen_pixmap_dir /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/share/coot/pixmaps INFO:: Colours file: /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/share/coot/colours.def loaded INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /programs/ccp4-6.2.0/lib/data/monomers/ There are 125 data in /programs/ccp4-6.2.0/lib/data/monomers//list/mon_lib_list.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/ALA.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/ASP.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/ASN.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//c/CYS.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/GLN.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/GLY.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/GLU.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//p/PHE.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//h/HIS.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//i/ILE.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//l/LYS.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//l/LEU.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//m/MET.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//m/MSE.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//p/PRO.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/ARG.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//s/SER.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//t/THR.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//v/VAL.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//t/TRP.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//t/TYR.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//p/PO4.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//s/SO4.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/GOL.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//e/ETH.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//c/CIT.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/AR.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//c/CR.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//c/CD.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/GD.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//t/TD.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//a/A.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//c/C.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//g/G.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//u/U.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//d/DA.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//d/DC.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//d/DG.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//d/DT.cif There are 2 data in /programs/ccp4-6.2.0/lib/data/monomers//h/HOH.cif There are 1 data in /programs/ccp4-6.2.0/lib/data/monomers//ener_lib.cif sbase monomer dir: . sbase files not found in . Reading coordinate file: /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/share/coot/standard-residues.pdb PDB file /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 *** glibc detected *** /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real: munmap_chunk(): invalid pointer: 0x0000000000d53dbc *** ======= Backtrace: ========= /lib64/libc.so.6(+0x753c6)[0x2b20088753c6] /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real(main+0x340)[0x544bd5] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b200881ecdd] /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real[0x542aa9] ======= Memory map: ======== 00400000-00f67000 r-xp 00000000 00:13 17151101 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real 01167000-011bc000 rw-p 00b67000 00:13 17151101 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real 011bc000-011d7000 rw-p 00000000 00:00 0 01504000-020a0000 rw-p 00000000 00:00 0 [heap] 2b1fff5d5000-2b1fff5f5000 r-xp 00000000 fd:00 131528 /lib64/ld-2.12.so 2b1fff5f5000-2b1fff5f7000 rw-p 00000000 00:00 0 2b1fff7f4000-2b1fff7f5000 r--p 0001f000 fd:00 131528 /lib64/ld-2.12.so 2b1fff7f5000-2b1fff7f6000 rw-p 00020000 fd:00 131528 /lib64/ld-2.12.so 2b1fff7f6000-2b1fff7f7000 rw-p 00000000 00:00 0 2b1fff7f7000-2b1fff81c000 r-xp 00000000 fd:00 140335 /usr/lib64/libpng12.so.0.49.0 2b1fff81c000-2b1fffa1c000 ---p 00025000 fd:00 140335 /usr/lib64/libpng12.so.0.49.0 2b1fffa1c000-2b1fffa1d000 rw-p 00025000 fd:00 140335 /usr/lib64/libpng12.so.0.49.0 2b1fffa1d000-2b1fffa1e000 rw-p 00000000 00:00 0 2b1fffa1e000-2b1fffaac000 r-xp 00000000 00:13 15508467 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguilegtk-2.0.so.0.1.0 2b1fffaac000-2b1fffcac000 ---p 0008e000 00:13 15508467 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguilegtk-2.0.so.0.1.0 2b1fffcac000-2b1fffcc3000 rw-p 0008e000 00:13 15508467 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguilegtk-2.0.so.0.1.0 2b1fffcc3000-2b1fffcc7000 r-xp 00000000 fd:00 132728 /lib64/libgthread-2.0.so.0.2200.5 2b1fffcc7000-2b1fffec6000 ---p 00004000 fd:00 132728 /lib64/libgthread-2.0.so.0.2200.5 2b1fffec6000-2b1fffec7000 rw-p 00003000 fd:00 132728 /lib64/libgthread-2.0.so.0.2200.5 2b1fffec7000-2b1ffffa6000 r-xp 00000000 00:13 2866001 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguile.so.17.4.0 2b1ffffa6000-2b20001a6000 ---p 000df000 00:13 2866001 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguile.so.17.4.0 2b20001a6000-2b20001ad000 rw-p 000df000 00:13 2866001 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libguile.so.17.4.0 2b20001ad000-2b20001bc000 rw-p 00000000 00:00 0 2b20001bc000-2b20001fb000 r-xp 00000000 00:13 25411220 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libgmp.so.3.4.4 2b20001fb000-2b20003fb000 ---p 0003f000 00:13 25411220 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libgmp.so.3.4.4 2b20003fb000-2b20003fc000 rw-p 0003f000 00:13 25411220 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libgmp.so.3.4.4 2b20003fc000-2b2000403000 r-xp 00000000 fd:00 132104 /lib64/libcrypt-2.12.so 2b2000403000-2b2000603000 ---p 00007000 fd:00 132104 /lib64/libcrypt-2.12.so 2b2000603000-2b2000604000 r--p 00007000 fd:00 132104 /lib64/libcrypt-2.12.so 2b2000604000-2b2000605000 rw-p 00008000 fd:00 132104 /lib64/libcrypt-2.12.so 2b2000605000-2b2000633000 rw-p 00000000 00:00 0 2b2000633000-2b200063a000 r-xp 00000000 00:13 15508469 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libltdl.so.3.1.5 2b200063a000-2b2000839000 ---p 00007000 00:13 15508469 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libltdl.so.3.1.5 2b2000839000-2b200083a000 rw-p 00006000 00:13 15508469 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libltdl.so.3.1.5 2b200083a000-2b200083b000 rw-p 00000000 00:00 0 2b200083b000-2b200083d000 r-xp 00000000 fd:00 157464 /lib64/libdl-2.12.so 2b200083d000-2b2000a3d000 ---p 00002000 fd:00 157464 /lib64/libdl-2.12.so 2b2000a3d000-2b2000a3e000 r--p 00002000 fd:00 157464 /lib64/libdl-2.12.so 2b2000a3e000-2b2000a3f000 rw-p 00003000 fd:00 157464 /lib64/libdl-2.12.so 2b2000a3f000-2b2000a7f000 r-xp 00000000 00:13 20668143 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-ccp4.so.2.0.7 2b2000a7f000-2b2000c7e000 ---p 00040000 00:13 20668143 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-ccp4.so.2.0.7 2b2000c7e000-2b2000c80000 rw-p 0003f000 00:13 20668143 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-ccp4.so.2.0.7 2b2000c80000-2b2000c82000 rw-p 00000000 00:00 0 2b2000c82000-2b2000c8c000 r-xp 00000000 00:13 6561096 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-cif.so.2.0.7 2b2000c8c000-2b2000e8c000 ---p 0000a000 00:13 6561096 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-cif.so.2.0.7 2b2000e8c000-2b2000e8d000 rw-p 0000a000 00:13 6561096 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-cif.so.2.0.7 2b2000e8d000-2b2000e8e000 rw-p 00000000 00:00 0 2b2000e8e000-2b2000e94000 r-xp 00000000 00:13 26293613 /home/programs/coot-Linux-x86_64-centos-6-gtk2-python/lib/libclipper-phs.so.2.0.7/programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot: line 245: 11400 Aborted $coot_real $@ coot-exe: "/programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real" coot-version: /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot-real platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report
smime.p7s
Description: S/MIME cryptographic signature
