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Installation issue: undefined symbol: PB_Ctzsymv #1

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randyzwitch opened this issue Feb 19, 2020 · 4 comments
Closed

Installation issue: undefined symbol: PB_Ctzsymv #1

randyzwitch opened this issue Feb 19, 2020 · 4 comments

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@randyzwitch
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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’
@randyzwitch
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Same issue is present with cloning from GitHub, and trying to build with GPU support.

@wrathematics
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Thanks for reporting this. My pbdSLAP build is broken. Try this one:

# make sure you have `make -j` set high before compiling
remotes::install_github("snoweye/pbdSLAP@single")

Then you should be able to install fmlr with this:

install.packages("fmlr", repos=c("https://hpcran.org", "https://cran.rstudio.com"))

And if you want to build with GPU support:

install.packages("fmlr", configure.args="--enable-gpu", repos=c("https://hpcran.org", "https://cran.rstudio.com"))

CC @snoweye your float build seems to be working

@wrathematics
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Oh and for GPU support, if CUDA is in a weird place, you will need to set the configure arg --with-cuda=/path/to/cuda. By default it will look in /usr/local/cuda.

@randyzwitch
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That fixed it for me, thanks! My CUDA is in a normal place, but I didn't run ldconfig, so after getting my install straightened out, the actual R packages installed just fine.

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@wrathematics @randyzwitch