search for: pymol

Anyone familiar with pymol? We're getting an error I find references to from a few years ago when we try to run remotely on a headless server. I can run it fine on my machine (CentOS 6.3, NVidia video), and on another person's workstation remotely, with other make video, but the server's got a Matrox - which sho...

Dear all,? I installed an software called pymol in my centos 6.7 system. The installation process seemed to be successful but when I initialized pymol, I got the following error:? import?_tkinter?#?If?this?fails?your?Python?may?not?be?configured?for?Tk ImportError:?libtk8.6.so:?cannot?open?shared?object?file:?No?such?file?or?directory. How could...

Dear Centos User I am trying to install package like 1) pymol 2 Xmgrace But unable install this package, showing this error. I search for this error in google, but the suggestions given there is not working for me. The same message showing for both software pakage. root at localhost tmp]# yum install grace Loaded plugins: fastestmirror, langpacks Loading mi...

Hi Jack, On Jan 25, 2009, at 10:00 AM, Jack Howarth wrote: > Doing that changes the error messages into a bus > error on the darwin linker. Pl. file bugzilla report (or radar) with a reproducible test case so that we can investigate this linker crash. As you know, one way to control symbol visibility is to use gcc's (inherited by llvm-gcc) visibility support. GCC supports, 1)

...- > Devang > > > > _______________________________________________ > LLVM Developers mailing list > LLVMdev at cs.uiuc.edu http://llvm.cs.uiuc.edu > http://lists.cs.uiuc.edu/mailman/listinfo/llvmdev Devang, I was surprised to discover that I could build all of pymol with -fvisibility=hidden using gcc 4.4 or llvm-gcc-4.2 with only a single header change... --- pymol-1.1/layer4/Cmd.h.orig 2009-01-30 18:58:58.000000000 -0500 +++ pymol-1.1/layer4/Cmd.h 2009-01-30 19:00:17.000000000 -0500 @@ -18,7 +18,8 @@ #include"os_python.h" -void init_cmd(v...

On Sun, Jan 25, 2009 at 11:38:48AM +0100, Jean-Daniel Dupas wrote: > > Le 25 janv. 09 à 06:01, Jack Howarth a écrit : > > > After trying the recommended use of -O4 -fvisibility=hidden to > > compile xplor-nih with full LTO optimizations, I discovered three > > symbols become undefined... > > > > llvm-gcc-4 -O4 -fvisibility=hidden -o xplor xplor.o \ >

I've had better luck compiling all of pymol 1.1r2 with -O4 on darwin9. Everythink links and there appears to be no regressions in the resulting code. I take it that LTO in llvm 2.5 is still limited to dead code elimination, correct? Will LTO ever be extended to inlining across files as well as constant-folding and global data allocation opti...

Jack Howarth wrote: > I've had better luck compiling all of pymol 1.1r2 with > -O4 on darwin9. Everythink links and there appears to be > no regressions in the resulting code. I take it that LTO > in llvm 2.5 is still limited to dead code elimination, > correct? No. libLTO does the equivalent to opt -internalize -ipsccp -globalopt -constmerge -dead...

Dear Centos Users We are running centos on our HPC. Indeed, we have a problem with running some software using X11 server such as pymol. For your information, we are using cygwin to access to the hpc (using ssh -X -Y username at xxx.xxx.xxx.xxx) When we are testing glxinfo on my desktop, it gives us the following error: [username at hpc ~]# glxinfo name of display: localhost:10.0 X Error of failed request: BadValue (integer param...

Does anyone have any insights into why clang ICEs when compiling layer2/RepCylBond.cpp in pymol at any optimization higher than -O0 on darwin? https://bugs.llvm.org/show_bug.cgi?id=37280 The problem is suppressed with -fno-strict-aliasing so I am wondering if there is some code in that file that could be re-organized to avoid the bug. Unfortunately, the ICE doesn't seem to indicate wha...