hi, as compiling, with the error:

[jlacosta@FIERA HYPHY_Source]$ ./build.sh
Usage: build.sh package_name
 where package_name is one of the following:
 SP : for a single threaded build
 MP : for a multi-threaded build with pthreads.
 MP2 : for a multi-threaded build with pthreads which support setconcurrency function.
 MPI : for a single-threaded build with MPI message passing support.
 DEBUG: single threaded debug version.
 LIBRARY [Python|R]: multi-threaded library version with optional wrappers for Python or R.
[jlacosta@FIERA HYPHY_Source]$ ./build.sh MPI
Linux
Checking for curl
Curl seems to be present
+-----------------------------------------------------------+
|Building a single-threaded HYPHYKernelMPI for MPI          |
+-----------------------------------------------------------+
COMPILER=g++, gcc
COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/home/jlacosta/Download/programas/HYPHY_Source/Source -I/home/jlacosta/Download/programas/HYPHY_Source/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__  -D __HYPHYMPI__
Building baseobj.cpp
In file included from baseobj.cpp:34:
batchlan.h:361:18: error: mpi.h: No such file or directory
baseobj.cpp: In function ‘bool GlobalShutdown()’:
baseobj.cpp:223: error: ‘MPI_COMM_WORLD’ was not declared in this scope
baseobj.cpp:223: error: ‘MPI_Comm_rank’ was not declared in this scope
baseobj.cpp:224: error: ‘MPI_Comm_size’ was not declared in this scope
baseobj.cpp:296: error: ‘MPI_Finalize’ was not declared in this scope
Error during compilation

Dear Luis,

This isn't a HyPhy bug.  Apparently your compiler can't find your MPI library.  Do you have one (e.g., MPICH, openMPI) installed on your machine?  Do you have a path to that library set for your compiler?

Cheers,
- Art.

Dear Luis,

One more thing to try: see if your machine has mpicc and mpic++ installed.
They will usually set all the correct include and library paths. If you have them,
then edit build.sh and set the COMPILER variable to mpic++ and COMPILERC to
mpicc.

If that does not work, you need to find mpi.h on your machine and update the
COMPILER_FLAGS variable in build.sh to include the -I/path/to/mpi.h

Cheers,
Sergei

Dear Sergei,
already installed MPICH, openMPI and edit build.sh and set the COMPILER variable to mpic++ and COMPILERC to  
mpicc but exists problem for compiling:

[jlacosta@FIERA HYPHY_Source]$ ./build.sh MPI
Linux
Checking for curl
Curl seems to be present
+-----------------------------------------------------------+
|Building a single-threaded HYPHYKernelMPI for MPI          |
+-----------------------------------------------------------+
COMPILER=mpic++, mpicc
COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/home/jlacosta/Download/programas/HYPHY_Source/Source -I/home/jlacosta/Download/programas/HYPHY_Source/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__  -D __HYPHYMPI__
File baseobj.cpp is up to date
File batchlan2.cpp is up to date
File batchlan.cpp is up to date
File bgm.cpp is up to date
File calcnode.cpp is up to date
File category.cpp is up to date
File error.cpp is up to date
File fisher_exact.cpp is up to date
File HYNetInterface.cpp is up to date
File hyphyunixutils.cpp is up to date
File likefunc.cpp is up to date
File list.cpp is up to date
File matrix.cpp is up to date
File Net.cpp is up to date
File nexus.cpp is up to date
File parser2.cpp is up to date
File parser.cpp is up to date
File polynoml.cpp is up to date
File regex.cpp is up to date
File scfg.cpp is up to date
File sequence.cpp is up to date
File site.cpp is up to date
File strings.cpp is up to date
File main-unix.cxx is up to date
SQLite File attach.c is up to date
SQLite File auth.c is up to date
SQLite File btree.c is up to date
SQLite File btree_rb.c is up to date
SQLite File build.c is up to date
SQLite File copy.c is up to date
SQLite File delete.c is up to date
SQLite File expr.c is up to date
SQLite File func.c is up to date
SQLite File hash.c is up to date
SQLite File insert.c is up to date
SQLite File main.c is up to date
SQLite File opcodes.c is up to date
SQLite File os.c is up to date
SQLite File pager.c is up to date
SQLite File parse.c is up to date
SQLite File pragma.c is up to date
SQLite File printf.c is up to date
SQLite File random.c is up to date
SQLite File select.c is up to date
SQLite File table.c is up to date
SQLite File tokenize.c is up to date
SQLite File trigger.c is up to date
SQLite File update.c is up to date
SQLite File util.c is up to date
SQLite File vacuum.c is up to date
SQLite File vdbe.c is up to date
SQLite File where.c is up to date
Linking HYPHYMPI
mpic++ -w -fsigned-char -o HYPHYMPI obj_MPI/attach.c.o obj_MPI/auth.c.o obj_MPI/baseobj.cpp.o obj_MPI/batchlan2.cpp.o obj_MPI/batchlan.cpp.o obj_MPI/bgm.cpp.o obj_MPI/btree.c.o obj_MPI/btree_rb.c.o obj_MPI/build.c.o obj_MPI/calcnode.cpp.o obj_MPI/category.cpp.o obj_MPI/copy.c.o obj_MPI/delete.c.o obj_MPI/error.cpp.o obj_MPI/expr.c.o obj_MPI/fisher_exact.cpp.o obj_MPI/func.c.o obj_MPI/hash.c.o obj_MPI/HYNetInterface.cpp.o obj_MPI/hyphyunixutils.cpp.o obj_MPI/insert.c.o obj_MPI/likefunc.cpp.o obj_MPI/list.cpp.o obj_MPI/main.c.o obj_MPI/main-unix.cxx.o obj_MPI/matrix.cpp.o obj_MPI/Net.cpp.o obj_MPI/nexus.cpp.o obj_MPI/opcodes.c.o obj_MPI/os.c.o obj_MPI/pager.c.o obj_MPI/parse.c.o obj_MPI/parser2.cpp.o obj_MPI/parser.cpp.o obj_MPI/polynoml.cpp.o obj_MPI/pragma.c.o obj_MPI/printf.c.o obj_MPI/random.c.o obj_MPI/regex.cpp.o obj_MPI/scfg.cpp.o obj_MPI/select.c.o obj_MPI/sequence.cpp.o obj_MPI/site.cpp.o obj_MPI/strings.cpp.o obj_MPI/table.c.o obj_MPI/tokenize.c.o obj_MPI/trigger.c.o obj_MPI/update.c.o obj_MPI/util.c.o obj_MPI/vacuum.c.o obj_MPI/vdbe.c.o obj_MPI/where.c.o -lssl -lcrypto -lcurl -lm -lmpich
/usr/bin/ld: cannot find -lmpich
collect2: ld returned 1 exit status
Finished

how to find -lmpich ?¿?

Dear Luis,

Since you are already using mpic++, delete the reference to lmpich (LINKER_FLAGS) from build.sh

Cheers,
Sergei

Dear Sergei,

already compiled, thank you very much!!!, but when doing analysis of recombination need an environment MPI view this failure:

***************** FILES IN 'Recombination' *****************


       (1) Screen an alignment using GARD (requires an MPI environment).
       (2) Process GARD results.
       (3) A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo].
       (4) Search an alignment for a single breakpoint.

Please select the file you want to use (or press ENTER to return to the list of analysis types):1
[ERROR] This analysis requires an MPI environment to run

as I enable MPI environment??¿
Sorry for the inconvenience...
JOSE LUIS

Hi Luis,

Did you execute HYPHYMPI in an MPI environment? i.e.:
> mpirun -np 3 ./HYPHYMPI

Cheers,
- Art.

Dear Luis,

You usually need to launch HyPhy as an mpi process. For mpich this is usually

[code]
$mpirun -np 8 ./HYPHYMPI arguments
[/code]

Cheers,
Sergei

Ha!  Beat you!   ;D

Art Poon wrote on May 15^th, 2008 at 3:00pm:

Ha!  Beat you!   ;D

1-1 it is  ;)