magma R package/library fails to build

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magma R package/library fails to build

Postby lejeczek » Mon Feb 24, 2014 5:36 am

dear all

I'm trying to install magma R package but build fails, I'm hoping you can help.
my MAGMA is built with gcc and ACML 5.3.1, build seems successful, I ran some tests from testing and all seem good (by the way, on AMD platforms it seems to be worth all the efforts to build with ACML, for CPU tests show results ~10 times better than with ATLAS only)
magma R fails:

/usr/local/cuda/bin/nvcc -c -arch=sm_13 -O2 -DADD_ -I/usr/local/cuda/include -I./include -Xcompiler "-O2 -DADD_ -fpic -I/local.native/include/R" magAriths.c -o magAriths.o
/usr/local/cuda/bin/nvcc -c -arch=sm_13 -O2 -DADD_ -I/usr/local/cuda/include -I./include -Xcompiler "-O2 -DADD_ -fpic -I/local.native/include/R" magFactors.c -o magFactors.o
/usr/local/cuda/bin/nvcc -c -arch=sm_13 -O2 -DADD_ -I/usr/local/cuda/include -I./include -Xcompiler "-O2 -DADD_ -fpic -I/local.native/include/R" magSolvers.c -o magSolvers.o
/usr/local/cuda/bin/nvcc -c -arch=sm_13 -O2 -DADD_ -I/usr/local/cuda/include -I./include -Xcompiler "-O2 -DADD_ -fpic -I/local.native/include/R" magUtils.c -o magUtils.o
/usr/local/cuda/bin/nvcc -shared -L/usr/local/cuda/lib64 -lcuda -lcublas -llapack -lmagmablas -lmagma magAriths.o magFactors.o magSolvers.o magUtils.o -o magma.so
/usr/bin/ld: cannot find -lmagmablas
/usr/bin/ld: cannot find -lmagma
collect2: error: ld returned 1 exit status
make: *** [magma.so] Error 1

libmagma.so is in my system-wide ld paths, I see it with ldconfig, yet builds fails as above
and cannot find anything like magmablas in my MAGMA build
I'm going to look for a help at R's end but before I do I thought I'd check if there is nothing wrong with my MAGMA build

any thoughts dear experts?
many thanks
lejeczek
 
Posts: 22
Joined: Tue Apr 09, 2013 2:57 am

Re: magma R package/library fails to build

Postby lejeczek » Mon Feb 24, 2014 12:28 pm

I realise I missed out path to magma libs, but how do I get hold of magmablas?
changelog reads "...Merge libmagmablas into libmagma to eliminate circular dependencies....."

is it rather R magma package that needs some work, updates?
would there be a workaround?

regards
lejeczek
 
Posts: 22
Joined: Tue Apr 09, 2013 2:57 am

Re: magma R package/library fails to build

Postby mgates3 » Tue Feb 25, 2014 6:40 pm

The libmagmablas library no longer exists -- its functionality was merged into libmagma. The R magma package therefore needs to be updated, but it should be a trivial update, just removing libmagmablas from the libraries.
-mark
mgates3
 
Posts: 388
Joined: Fri Jan 06, 2012 2:13 pm

Re: magma R package/library fails to build

Postby lejeczek » Wed Feb 26, 2014 5:45 am

yes, apologies, I found that out later and contacted Rmagma's author
thanks
lejeczek
 
Posts: 22
Joined: Tue Apr 09, 2013 2:57 am


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