Question: Installing Bwa On 32 Bit Unix Machine
0
gravatar for always_learning
5.6 years ago by
Doha, Qatar
always_learning960 wrote:

Hi All,

I was able to install bwa easily on 64 bit but while I was trying to install on 32 bit, its saying an error.

[uvj@localhost bwa-0.7.5a]$ make

gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o

In file included from ksw.c:28:

/usr/lib/gcc/i686-redhat-linux/4.4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"

ksw.c:48: error: expected specifier-qualifier-list before ‘__m128i’

I tried these recommendation at this website:

http://sourceforge.net/mailarchive/forum.php?thread_name=86A911D6-DEE2-49F4-81CA-529FFB53A359%40sanger.ac.uk&forum_name=bio-bwa-help

but still didn't work !!

Any input on this ?

bwa • 6.7k views
ADD COMMENTlink modified 5.6 years ago by Pierre Lindenbaum119k • written 5.6 years ago by always_learning960
3
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Here are the first lines of my Makefile:

bwa-0.7.4$ more Makefile 
    CC=            gcc
    CFLAGS=        -g -Wall -O2 -msse -mmmx -msse2
    AR=            ar
    DFLAGS=        -DHAVE_PTHREAD
    LOBJS=        utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pai
    r.o
    AOBJS=        QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlit
    e.o \
                is.o bwtindex.o bwape.o kopen.o pemerge.o \
                bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
                bwtsw2_chain.o fastmap.o bwtsw2_pair.o
    PROG=        bwa
    INCLUDES=    
    LIBS=        -lm -lz -lpthread
    (...)
ADD COMMENTlink modified 3 months ago by RamRS21k • written 5.6 years ago by Pierre Lindenbaum119k

Thanks !! It works !! But can you please explains these changes you made in makefile actually:

  1. CFLAGS= -g -Wall -O2 -msse -mmmx -msse2
  2. DFLAGS= -DHAVE_PTHREAD
ADD REPLYlink modified 3 months ago by RamRS21k • written 5.6 years ago by always_learning960
  1. I think I got that problem http://stackoverflow.com/questions/16410149
  2. allow multithreading
ADD REPLYlink modified 3 months ago by RamRS21k • written 5.6 years ago by Pierre Lindenbaum119k

Thanks !! Some of feature of SSE is not available for 32 bits and SSE is basically supporting 64 bits by design only.

ADD REPLYlink modified 3 months ago by RamRS21k • written 5.6 years ago by always_learning960
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