HyPhy message board - Problem Compiling HyPHy MP Ubuntu 12.04

Austin Meyer

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Problem Compiling HyPHy MP Ubuntu 12.04
Jul 5^th, 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:

[ 50%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/matrix.cpp.o
/home/ausmeyer/Desktop/hyphy/src/core/matrix.cpp: In member function ‘void _Matrix::Multiply(_Matrix&, _Matrix&)’:
/home/ausmeyer/Desktop/hyphy/src/core/matrix.cpp:3680:26: error: ‘secondArg’ not specified in enclosing parallel
/home/ausmeyer/Desktop/hyphy/src/core/matrix.cpp:3679:9: error: enclosing parallel
/home/ausmeyer/Desktop/hyphy/src/core/matrix.cpp:3702:94: error: ‘storage’ not specified in enclosing parallel
/home/ausmeyer/Desktop/hyphy/src/core/matrix.cpp:3679:9: error: enclosing parallel
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/matrix.cpp.o] Error 1
make[2]: *** [CMakeFiles/HYPHYMP.dir/all] Error 2
make[1]: *** [CMakeFiles/MP2.dir/rule] Error 2
make: *** [MP2] Error 2

I'm not sure if this is a bug or not? Any suggestions?

Thanks,

Austin

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Sergei

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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #1 - Jul 5^th, 2012 at 1:16pm

Hi Austin,

Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login (there is a fix in the comments)
I added a more generic fix it in the current HyPhy source base that you can d/l from Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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Austin Meyer

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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #2 - Jul 6^th, 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

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #3 - Jul 6^th, 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
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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #4 - Sep 1^st, 2012 at 7:10am Sergei, Your fork is more current than the veg?
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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #5 - Sep 1^st, 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.

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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #6 - Sep 13^th, 2012 at 2:42pm Sergei?? Anyone???
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #7 - Sep 14^th, 2012 at 11:28am Sorry, grant season:( The most current fork is here: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login Sergei
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jackson

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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #8 - Sep 16^th, 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

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #9 - Sep 17^th, 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
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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: Problem Compiling HyPHy MP Ubuntu 12.04 Reply #10 - Sep 23^rd, 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...
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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #11 - Sep 24^th, 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__)

and replace it with

Code:

add_definitions(-D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHY_NO_CURL__)

Sergei

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jackson

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Re: Problem Compiling HyPHy MP Ubuntu 12.04
Reply #12 - Oct 9^th, 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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