Getting executable "raxmlHPC-SSE3"

[Spencer Hall]

Hello,

I have downloaded RAxML and am attempting to use it to get the executable command raxmlHPC-SSE3. In order to do this, I have followed the instructions at the Exelixis Lab website (http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html), which say that the following command will create that executable:

$ make -f Makefile.SSE3.gcc

I have used this command, and followed it with this sequence:

$ cd /usr/local/raxml/latest/

$ ls

However, the only files/executables listed in this directory are:

manual  raxml  raxmlHPC  raxmlHPC-MPI  raxmlHPC-PTHREADS  README

I noticed that at the very beginning of the compilation from the "make -f Makefile.SSE3.gcc" command, there was a line that seemed to be removing the raxmlHPC-SSE3 executable:

rm -f *.o raxmlHPC-SSE3

Can anyone explain how to get this executable to be available under the /usr/local/raxml/latest/ directory?

Thanks,

Spencer

[Alexey Kozlov]

Dear Spencer,

it looks like raxmlHPC-SSE3 compilation terminated with an error, could you please post your make output?

> I noticed that at the very beginning of the compilation from the "make -f Makefile.SSE3.gcc" command, there was a line
> that seemed to be removing the raxmlHPC-SSE3 executable:
>
> rm -f *.o raxmlHPC-SSE3

Yes, we added this cleanup step recently to avoid confusion with stale object files.
However, raxmlHPC-SSE3 must be re-generated upon successful compilation.

Best,
Alexey

[Alexandros Stamatakis]

Hi Spencer,

Where did you download the RAxML source code from?

Are you sure you copied the source files into the folder
/usr/local/raxml/latest/ ?

Also, why don't you install and run the test locally under your private
directory?

Cheers,

Alexis

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Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Spencer Hall]

Unfortunately I did not save the output from the compilation of the software; I tried to unzip the file and reinstall it, but this did not work, so I don't have the make output. How is raxmlHPC-SSE3 regenerated upon compilation?

[Spencer Hall]

Hi Alexis,

I downloaded it from the RAxML github, although I don't recall if I copied it into the /usr/local/raxml/latest/ folder. Currently if I perform the ls command for that folder, it shows the executables I listed above, but not the raxmlHPC-SSE3.

Earlier I was looking at the contents of the standard-RAxML-master directory and found that the raxmlHPC-SSE3 executable was actually under that larger directory, though not under the /usr...etc. directory. Is there a way to simply move it from one to the other?

[Spencer Hall]

Actually, I was able to re-compile it just now. Here is the make output for make -f Makefile.SSE3.gcc:

 rm -f *.o raxmlHPC-SSE3
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o axml.o axml.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o optimizeModel.o optimizeModel.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o multiple.o multiple.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o searchAlgo.o searchAlgo.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o topologies.o topologies.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o parsePartitions.o parsePartitions.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o treeIO.o treeIO.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o models.o models.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o bipartitionList.o bipartitionList.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o rapidBootstrap.o rapidBootstrap.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o evaluatePartialGenericSpecial.o evaluatePartialGenericSpecial.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o evaluateGenericSpecial.o evaluateGenericSpecial.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o newviewGenericSpecial.o newviewGenericSpecial.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o makenewzGenericSpecial.o makenewzGenericSpecial.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o classify.o classify.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o fastDNAparsimony.o fastDNAparsimony.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o fastSearch.o fastSearch.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o leaveDropping.o leaveDropping.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o rmqs.o rmqs.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o rogueEPA.o rogueEPA.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o ancestralStates.o ancestralStates.c
gcc  -D__SIM_SSE3   -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops     -c -o mem_alloc.o mem_alloc.c
gcc  -c -o eigen.o eigen.c
gcc  -o raxmlHPC-SSE3 axml.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 fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  -lm 

[Alexandros Stamatakis]

great :-) so I guess the issue is closed,

alexis

[Spencer Hall]

Well, no, the code is still giving the error message - I meant that I had re-compiled it so that you could check the output to make sure nothing was going wrong with it.

This is the error message I'm getting (the file is an R file which references the RAxML software):

> for(i in 1:nindividual)
+ {
+         try(system(paste("/usr/local/raxml/latest/raxmlHPC-SSE3 -m GTRGAMMA -n ", paste("con",i,sep=""), " -f b -t ", paste("RAxML_bestTree.ind", i,sep=""), " -z ", paste("RAxML_bootstrap.bootind",i,sep=""))))
+ }
sh: /usr/local/raxml/latest/raxmlHPC-SSE3: No such file or directory

[Alexandros Stamatakis]

does it find it when you type:

/usr/local/raxml/latest/raxmlHPC-SSE3

if yes, then you are either running the R script in a different file
system (different machine) or the R call syntax is incorrect, but I am
no R expert,

alexis

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> <https://groups.google.com/d/optout>.

>
> --
> 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 <http://www.exelixis-lab.org>

[Spencer Hall]

At present, Linux is not returning anything for that command. I switched the directory to /usr/local/raxml/latest/, and used the ls command to list the available files and executables, which returned this list:

manual  raxml  raxmlHPC  raxmlHPC-MPI  raxmlHPC-PTHREADS  README

So it looks like raxmlHPC-SSE3 is not being installed for some reason. Is there something in addition to using the Makefile that I need to do to make this executable available?

[William Gearty]

Have you made sure to run rm *.o after making one of the executables?

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[Alexey Kozlov]

So why don't you just copy the raxmlHPC-SSE3 executable from the folder where you've compiled it (i.e. the place where
you unpacked the RAxML sources and ran "make -f Makefile.SSE3.gcc") to the /usr/local/raxml/latest/?

Or alternatively, just change the path in your R code so that it points to the aforementioned folder instead of
/usr/local/raxml/latest/.

> > www.exelixis-lab.org <http://www.exelixis-lab.org> <http://www.exelixis-lab.org>

[Spencer Hall]

Yes, I have run rm*.o after running the make -f Makefile.SSE3.gcc command; the output indicated that this command went through without an error message, but the raxmlHPC-SSE3 executable is still absent from the relevant directory.

[Spencer Hall]

I have tried that as well, however, changing the path seems to disrupt another part of the code, though I am not sure why, as they deal with separate software components.

[Alexey Kozlov]

so once again:

- what is the path to the folder where you have RAxML sources and where you run make?
- do you have raxmlHPC-SSE3 executable in this folder (ls raxmlHPC-SSE3)?
- can you copy this executable to /usr/local/raxml/latest/, or you don't have write permissions?

> I have tried that as well, however, changing the path seems to disrupt another part of the code, though I am not sure
> why, as they deal with separate software components.

so which error exactly do you get? is it related to RAxML or might be a completely independent error on the subsequent
processing step?