Running RAxML on FreeBSD

[Hrishikesh Lokhande]

Hello all,

I am trying to complie RaXML on a FreeBSD machine. After searching I got only one hit relevant to this operation system.

The version that I have is RAxML-7.2.8-ALPHA, I am not aware whether this is a stable version. If there is any stable version compatible to my operating system please let me know. 

During compiling I get the following.

[hrishi@#### ~/RAxML-7.2.8-ALPHA]$ make -f Makefile.gcc 

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c axml.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c raxmlParsimony.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c optimizeModel.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c multiple.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c searchAlgo.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c topologies.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c parsePartitions.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c treeIO.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c models.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c bipartitionList.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c rapidBootstrap.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c evaluatePartialGenericSpecial.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c evaluateGenericSpecial.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c newviewGenericSpecial.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c makenewzGenericSpecial.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c classify.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c mesh.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c fastDNAparsimony.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c fastSearch.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c leaveDropping.c

gcc -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse -c rogueEPA.c

gcc -o raxmlHPC axml.o raxmlParsimony.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o mesh.o fastDNAparsimony.o fastSearch.o leaveDropping.o rogueEPA.o -lm

axml.o(.text+0x1a): In function `malloc_aligned':

: undefined reference to `posix_memalign'

*** Error code 1

Stop in /usr/home/hrishi/RAxML-7.2.8-ALPHA.

Is there any solution to fix this? 

[Alexandros Stamatakis]

Try to google:

"undefined reference to `posix_memalign' freeBSD" it looks as if a
library has not been installed properly.

The most up to date version of RAxML is available here:

https://github.com/stamatak/standard-RAxML

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org