Compilation time and memory

[inab]

Compilation time and memory

[scapella]

Dear Bernardo,

Thank you for giving a try to trimAl.

I'm looking on this issue but so far I haven't found a solution.
According to your log, you have been able to compile "readal", a program
for dealing with multiple sequence alignment.
Could you please see whether this binary is working or not?. If it's
working, the problem may be on trimAl main.cpp file.

As soon as I get a satisfactory solution for this problem, I'll get you
back.
Cheers,

S

On Fri, Aug 2, 2013 at 12:33 PM, BernardoBello [email protected]:

Hi,

While compilation, I had t stop because the make command was using all my
system memory (12 GB). Is that normal? Below is where I had to stop the
compilation process.

I'm running MACOSX Lion.

Thank you,

Bernardo

dhcp-172-17-27-227:source bernardo$ make
g++ -Wall -O2 -c alignment.cpp rwAlignment.cpp autAlignment.cpp
g++ -Wall -O2 -c statisticsGaps.cpp
g++ -Wall -O2 -c utils.cpp
g++ -Wall -O2 -c similarityMatrix.cpp
g++ -Wall -O2 -c statisticsConservation.cpp
g++ -Wall -O2 -c sequencesMatrix.cpp
g++ -Wall -O2 -c compareFiles.cpp
g++ -Wall -O2 -o readal readAl.cpp -lm alignment.o statisticsGaps.o
utils.o similarityMatrix.o statisticsConservation.o sequencesMatrix.o
compareFiles.o
g++ -Wall -O2 -o trimal main.cpp -lm alignment.o statisticsGaps.o utils.o
similarityMatrix.o statisticsConservation.o sequencesMatrix.o compareFiles.o

^Cmake: *** [trimal] Interrupt: 2

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6
.

S

[BernardoBello]

Hi,

readal seems to be working fine, at least I can see the Basic usage:

Bernardos-MacBook-Pro:source bernardo$ ./readal

readAl v1.4.rev12 build[2013-06-25]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón.

readAl webpage: http://trimal.cgenomics.org

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, the last available version.

Basic usage
readal -in -out [options].

-h                   Show this information.
--version            Show readAl version.

-in <inputfile>      Input file in several formats.
-out <outputfile>    Output file name (default STDOUT).

-format              Print information about input file format and if sequences are aligned or not.
-type                Print information about biological sequences datatype (e.g. nucleotides:dna, nucleotides:rna, aminoacids, etc)
-info                Print information about sequences number, average sequence length, max & min sequence length

-onlyseqs            Generate output with only residues from input file

-html                Output residues colored according their physicochemical properties. HTML file.

-reverse             Output the reverse of sequences in input file.

-nbrf                Output file in NBRF/PIR format
-mega                Output file in MEGA format
-nexus               Output file in NEXUS format
-clustal             Output file in CLUSTAL format

-fasta               Output file in FASTA format
-fasta_m10           Output file in FASTA format. Sequences name up to 10 characters.

-phylip              Output file in PHYLIP/PHYLIP4 format
-phylip_m10          Output file in PHYLIP/PHYLIP4 format. Sequences name up to 10 characters.
-phylip_paml         Output file in PHYLIP format compatible with PAML
-phylip_paml_m10     Output file in PHYLIP format compatible with PAML. Sequences name up to 10 characters.
-phylip3.2           Output file in PHYLIP3.2 format
-phylip3.2_m10       Output file in PHYLIP3.2 format. Sequences name up to 10 characters.

Bernardos-MacBook-Pro:source bernardo$

[scapella]

After some testing, I realized this problem seems to be related to the optimization (-O2 flag) so removing this from the makefile should make the job.