fml-fam/fmlr

R bindings for the Fused Matrix Library (fml)

fmlr's Issues

Installation issue: undefined symbol: PB_Ctzsymv

I tried to install the stable CPU version, but ran into the following error on Ubuntu 18.04LTS:

> install.packages("fmlr", repos=c("https://hpcran.org", "https://cran.rstudio.com"))
Installing package into ‘/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://hpcran.org/src/contrib/fmlr_0.1-0.tar.gz'
Content type 'application/x-gzip' length 131299 bytes (128 KB)
==================================================
downloaded 128 KB

* installing *source* package ‘fmlr’ ...
** using staged installation
configure: not using GPU
 
******************* Results of fmlr package configure *******************
 
* R Report:
    >> R_CPPFLAGS=-I/usr/share/R/include
    >> FLOAT_LIBS=-L/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/libs -l:float.so -Wl,-rpath=/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/libs
    >> FLOAT_INCL=-I/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include
* GPU Report:
    >> not used
* MPI report:
    >> SPMD_CPPFLAGS = -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI
    >> SPMD_LDFLAGS = -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi  -lutil -lpthread
    >> SLAP_LDFLAGS = /home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/pbdSLAP/lib/libslap.a $(LAPACK_LIBS) $(BLAS_LIBS)
*************************************************************************
 
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/02-features.r
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmlr-native.c -o fmlr-native.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cpumat.cpp -o cpumat.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cpuvec.cpp -o cpuvec.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c helpers-cpu.cpp -o helpers-cpu.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c linalg-cpu.cpp -o linalg-cpu.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c grid.cpp -o grid.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c helpers-mpi.cpp -o helpers-mpi.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c linalg-mpi.cpp -o linalg-mpi.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mpimat.cpp -o mpimat.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -I"/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/float/include"  -I/usr/lib/x86_64-linux-gnu/openmpi/include  -DMPI2 -DOPENMPI -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gpu-dummy-bindings.cpp -o gpu-dummy-bindings.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fmlr.so fmlr-native.o cpumat.o cpuvec.o helpers-cpu.o linalg-cpu.o grid.o helpers-mpi.o linalg-mpi.o mpimat.o gpu-dummy-bindings.o /home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/pbdSLAP/lib/libslap.a -llapack -lblas -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lutil -lpthread -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR
installing to /home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-fmlr/00new/fmlr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'as_gpuvec(v, copy = FALSE)': unused argument (copy = FALSE) 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘fmlr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-fmlr/00new/fmlr/libs/fmlr.so':
  /home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-fmlr/00new/fmlr/libs/fmlr.so: undefined symbol: PB_Ctzsymv
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/rzwitch/R/x86_64-pc-linux-gnu-library/3.6/fmlr’
Warning in install.packages :
  installation of package ‘fmlr’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpbzXFnd/downloaded_packages’

GPU on Windows

I do not have the ability to test this, but I think the package can now be built with GPU backend support on Windows. I would appreciate any input/feedback on this.

If you are willing to test, you can download the development version of the package with git (there are submodules so install_github()-like things won't work):

git clone --recurse-submodules https://github.com/fml-fam/fmlr.git

Modify the first 2 lines of src/Makevars.win. The first should be set to USE_GPU = "TRUE". The second should be set to whatever your CUDA path is. The contents should be include, lib, etc. Actually, just giving me an ls of that path would be very helpful.

Install the package dependencies as needed:

install.packages("R6")
install.packages("float")

Next, try to install the package:

R CMD INSTALL fmlr/

Here's a basic test you can run to see if it works:

suppressMessages(library(fmlr))
c = card()
c

x = gpumat(c, 3, 2)
x$fill_linspace(1, 6)
x$info()
x

Here's an example of the output I see on my Linux box:

## GPU 0 (GeForce GTX 1070 Ti) 821/8116 MB - CUDA 10.1

# gpumat 3x2 type=d 
1.0000 4.0000 
2.0000 5.0000 
3.0000 6.0000