Dear zhuocheng,

Running HYPHYMP in an MPI environment is not going to make use of MPI libraries; it will simply run a single process on the master node. That said, what you are seeing is still abnormal. What is the Operating System on your cluster?

Try running HYPHYMP on BatchFiles/speedtest.bf to make sure the code executes correctly on an example analysis. I have seen the 'bad symbols' error as a result of compiling with 'char' (a C type) being treated as 'unsigned' by default. There should be a compiler flag (depending on what system you have), that forces 'char' to be 'signed' by default. Please make sure that flag is add to the GCC compiler options string in the build.sh script. This should already be done for gcc/Linux and a few other distributions.

Cheers,
Sergei

If I directly run HYPHYMP, that's say, use ./HYPHYMP  and then, I can run HYPHYMP and also can run speedtest.bf. However, if I run the HYPHYMP by using the mpirun np -10 /HYPHYMP BASEPATH .... as the manual denote, I would find the errors as above.

If I directly run HYPHYMP and then run GABranch, I get the follwoing information and at last, it's wrong.

homopan:~/HyPhy/HYPHY_Source zchou$ ./HYPHYMP
  /HYPHY 1.0020080115beta(MP) for Darwin on Power Macintosh\ 
***************** TYPES OF STANDARD ANALYSES *****************


       (1) Basic Analyses
       (2) Codon Selection Analyses
       (3) Compartmentalization
       (4) Data File Tools
       (5) Miscellaneous
       (6) Model Comparison
       (7) Kernel Analysis Tools
       (8) Molecular Clock
       (9) Phylogeny Reconstruction
       (10) Positive Selection
       (11) Recombination
       (12) Selection/Recombination
       (13) Relative Rate
       (14) Relative Ratio
       (15) Substitution Rates

Please select type of analyses you want to list (or press ENTER to process custom batch file):

/Volumes/chicken/Users/zchou/HyPhy/HYPHY_Source/Batch file to run::/Users/zchou/HyPhy/GABranchFiles/ModelSelectorBranchLocal.bf


                       +-------------------+
                       |Choose Genetic Code|
                       +-------------------+


       (1):[Universal] Universal code. (Genebank transl_table=1).
       (2):[Vertebrate mtDNA] Vertebrate mitochondrial DNA code. (Genebank transl_table=2).
       (3):[Yeast mtDNA] Yeast mitochondrial DNA code. (Genebank transl_table=3).
       (4):[Mold/Protozoan mtDNA] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).
       (5):[Invertebrate mtDNA] Invertebrate mitochondrial DNA code. (Genebank transl_table=5).
       (6):[Ciliate Nuclear] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).
       (7):[Echinoderm mtDNA] Echinoderm mitochondrial DNA code. (Genebank transl_table=9).
       (8):[Euplotid Nuclear] Euplotid Nuclear code. (Genebank transl_table=10).
       (9):[Alt. Yeast Nuclear] Alternative Yeast Nuclear code. (Genebank transl_table=12).
       (10):[Ascidian mtDNA] Ascidian mitochondrial DNA code. (Genebank transl_table=13).
       (11):[Flatworm mtDNA] Flatworm mitochondrial DNA code. (Genebank transl_table=14).
       (12):[Blepharisma Nuclear] Blepharisma Nuclear code. (Genebank transl_table=15).

Please choose an option (or press q to cancel selection):1

/Users/zchou/HyPhy/GABranchFiles/Codon file to analyze::/Users/zchou/HyPhy/GABranchFiles/Example/lysozyme.nex


A tree was found in the data file:
(((((LANGUR_SEN_SVE,LANGUR_TOB_TFR,DOUC_LANGUR_PNE),PROBISCIS_NLA),COLOBUS_CGU_C
AN),(((BABOON_PCY,MANGABEY_CAT),RHESUS_MMU),ALLEN_ANI,(TALAPOIN_MTA,(PATAS_EPA,V
ERVET_CAE)))),(((HUMAN,CHIMP_BONOBO_GORILLA),ORANGUTAN_PPY),GIBBON_GGO),(SQUIRRE
L_M,(TAMARIN_SOE,MARMOSET_CJA)))

Would you like to use it:(Y/N)?y



Nucleotide a 6-character model string specification (e.g. HKY85 = 010010):?

Nucleotide a 6-character model string specification (e.g. HKY85 = 010010):?010010 
[Preliminary Step 1] A total of 33 branches. Fitting a nucleotide model to approximate branch lengths...
[Preliminary Step 2] Nucleotide LogL = -1062.28
[Preliminary Step 3] Base model has 44 parameters. Log-L = -1038.75. Mean dN/dS = 0.568085
Error:
Invalid Matrix Index [0][0] in a -2 by 2 matrix.
Current BL Command:sortedScores[0][0]=-crapAIC

Check errors.log for details on execution errors.

Check messages.log details of this run.
HYPHYMP(8368) malloc: *** error for object 0x2813e00: pointer being reallocated was not allocated
HYPHYMP(8368) malloc: *** set a breakpoint in szone_error to debug
Error:
Memory Full Exiting...
Current BL Command:sortedScores[0][0]=-crapAIC

Check errors.log for details on execution errors.

Check messages.log details of this run.

Hi Sergei,

Thanks. I had add the path to the mpi.h, but the fail information as follows:

....
Linking HYPHYMPI
g++ -w -fsigned-char -o HYPHYMPI obj_MPI/HYNetInterface.cpp.o obj_MPI/Net.cpp.o obj_MPI/attach.c.o obj_MPI/auth.c.o obj_MPI/baseobj.cpp.o obj_MPI/batchlan.cpp.o obj_MPI/batchlan2.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/hyphyunixutils.cpp.o obj_MPI/insert.c.o obj_MPI/likefunc.cpp.o obj_MPI/list.cpp.o obj_MPI/main-unix.cxx.o obj_MPI/main.c.o obj_MPI/matrix.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/parser.cpp.o obj_MPI/parser2.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: can't locate file for: -lmpich
collect2: ld returned 1 exit status
Finished