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HYPHY Package >> HyPhy bugs >> Problem Compiling HyPHy MP Ubuntu 12.04 http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1341519237 Message started by Austin Meyer on Jul 5th, 2012 at 1:13pm |
Title: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Austin Meyer on Jul 5th, 2012 at 1:13pm
I can't seem to get MP to compile on Ubuntu 12.04 using several compilers (4.4, 4.5, 4.6).
The error is the following: Quote:
I'm not sure if this is a bug or not? Any suggestions? Thanks, Austin |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Austin Meyer on Jul 6th, 2012 at 6:55am
Thanks, the forum post worked.
I think I actually had the most recent git commit when I was trying to compile it before... here is the commit that wasn't working for me: commit ad50c1e73f5d97765627184be0fd307edcc87ae8 Author: Sergei L Kosakovsky Pond <spond@ucsd.edu> Date: Tue Jun 19 11:17:20 2012 -0700 Was there a patch I missed somewhere? Thanks for the help, Austin |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Sergei on Jul 6th, 2012 at 9:22am
Hi Austin,
Sorry -- I meant for you to grab the git commit from my fork (/spond not /veg). At any rate, I'll push the fix to the main branch soon. Sergei |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Sep 1st, 2012 at 7:10am
Sergei,
Your fork is more current than the veg? |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Sep 1st, 2012 at 2:28pm
Sergei,
After compilation, when I try running HYPHYMPI, I've got this message ./HYPHYMPI: /usr/local/lib/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by ./HYPHYMPI)" Are missing anything? In attachment a file with the compilation. The uname -r Linux jackson-desktop 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux Ubuntu 12.04. http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=HYPHY_Compilation.txt (10 KB | 0
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Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Sep 13th, 2012 at 2:42pm
Sergei?? Anyone???
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Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Sergei on Sep 14th, 2012 at 11:28am |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Sep 16th, 2012 at 10:26am
Thanks Sergei.
I compiled the most current version, but I keep getting the message: ./HYPHYMPI: /usr/local/lib/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by ./HYPHYMPI)" What do you think can be? Another question, I installed version 2.1.2 for Windows, when I go into options, does not appear able to select how many cores the cpu I can use, is this normal? The windows version uses more than one core in multi-core processors? Thanks. Cheers |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Sergei on Sep 17th, 2012 at 4:33pm
Hmm, I haven't seen this libcurl issue before.
Do you have libcurl-developer installed? The Windows version is single-threaded at the moment; we are migrating the whole GUI codebase to use Qt, so this issue should be temporary. Sergei |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Sep 23rd, 2012 at 8:54am
Sergei,
I have installed the latest versions of developer packages. I've installed this package libcurl4-openssl-dev. Not conformed to this situation, I compiled OpenSSL and the CURL package, more updated versions, and yet still encountering this error when I run the command to run the HYPHY... :'( :'( :'( :'( :'( :'( |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by Sergei on Sep 24th, 2012 at 10:03am
Hi Jackson,
Sorry for your troubles! This must be very frustrating. I think it may be best at this point to simply turn off CURL support in HyPhy, by adding a define for __HYPHY_NO_CURL__ into the config file. Just search CMakeLists.txt for Code (] add_definitions(-D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__) [/code):
Sergei |
Title: Re: Problem Compiling HyPHy MP Ubuntu 12.04 Post by jackson on Oct 9th, 2012 at 7:55am
Sergei,
It worked for me. Another question, I have compiled version MP for the HYPHY wore the 8-core computer, but when I run the program, it only uses 1. Then tried compliar MPI, so using the command mpi-run -np 8, to use all 8 cores, gives an error because it tries to connect to the other nodes. When I compile the MrBayes or even PhyML so that both utilize multiple cores, the command mpi-run only on the local machine is not connected to another node. Am I doing something wrong? |
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