On 04/07/2011 02:32 PM, Leonid Flaks wrote:
On 04/07/2011 02:23 AM, Kay Diederichs wrote:Am 20:59, schrieb Leon Flaks:I am running coot on 64-bit Fedora 14 installed from binaries compiled for centos 5 with both gtk and python. I made a number of links to so libraries somewhat similar to the ones described on this list last month. However, there is another issue I ran into, which prevented coot from starting. selinux is enabled and it is complaining about executable stack set on the library libgmp.so.3 . This library comes with coot tarbal. There is another copy of the same library on the system which has this flag set properly, but of course, coot uses the one that comes with it. To fix this issue I had to run 'execstack -c $coot_root_dir/lib/libgmp.so.3.3.0', which solved my problem. Coot is installed on the nfs server, so this command had to be executed on the server as root. Coot is happy after that and runs without problems. However, every time I download the new version (I tried 3455 yesterday), I have to fix this stack flag. Would it be possible to get it done on the server, so that binaries that come with the tarbal have it fixed already?Thanks, Leonwhy not simply delete coot's version of libgmp.so.3.3.0 after downloading it? coot then should find and use the system-supplied library. HTH, KayThanks for the reply! I'll test it next week. But how is your suggestion any better then the one I was doing? rm command is shorter then execstack ;-) but you need to remove the link to libgmp.so.3 also. Would it be better to have it fixed in the binary? Leon
Leon,I suppose it's better since you can "fix" it yourself with ordinary user privileges - IOW you don't need to bother your system administrator with it. (I don't understand why a link to libgmp.so.3 has to be removed.)
"fix in the binary" ? - the binary is built for CentOS-5, whereas you run FC14. I'm not sure if running 'execstack -c $coot_root_dir/lib/libgmp.so.3.3.0' will not have undesirable side effects on CentOS-5 machines.
The proper way might be to compile&link on a FC14 machine. But that boils down to the question for which platforms there have to be separate builds ... have you counted the existing ones?
best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [email protected] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".
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