openblas centos problem of installation and use

[xuyan-piestat]

my os is centos 6.6 ,when i make for openblas .at last error is :
linktest.c:(.text+0x3218): undefined reference to zlatme_' linktest.c:(.text+0x321f): undefined reference to zlatmr_'
linktest.c:(.text+0x3226): undefined reference to zlatms_' linktest.c:(.text+0x322d): undefined reference to zlatmt_'
collect2: ld returned 1 exit status
make[1]: *** [../libopenblas_haswellp-r0.2.19.so] Error 1
make[1]: Leaving directory `/home/OpenBLAS-0.2.19/exports'

why?

then i can make install to /opt/openblas
when i use R language to test openblas，
update-alternatives --config libblas.so.3，no any output,
i have installed blas and openblas
blas is in /usr/lib64
openblas is in /opt/openblas

go to r shell
x <- matrix(1:(3000 * 3000), 3000, 3000)

system.time(tmp <- x %% x)
user system elapsed
38.817 0.061 38.866
i force to subtitude libblas.so.3 to openblas version
unlink /usr/lib64/libblas.so.3
ln -s ln -s /opt/OpenBLAS/lib/libopenblas.so /usr/lib64/libblas.so.3
unlink /usr/lib64/liblapack.so.3
ln -s /opt/OpenBLAS/lib/libopenblas.so /usr/lib64/openblas/liblapack.so.3
system.time(tmp <- x %% x)
user system elapsed
35.217 0.049 35.255
echo $LD_LIBRARY_PATH , result is
/home/data2/daqi/pcre-8.39/lib:/home/data2/daqi/xz-5.2.2/lib:/home/data2/daqi/hdf5-1.8.8/lib:/usr/local/lib64/R/lib:/usr/local/lib:/usr/lib:/usr/lib64:

both almost have no difference . I donot know why.
anyone tell me which step is wrong in my process.

[brada4]

Build error:
seek OpenBLAS FAQ which tells how to acquire recent binutils on CentOS 6
Then make clean before next build, and make sure to attach full build log, as the missing files are consequence of earlier errors.

R configuration:
Fedora has no alternatives mechanism for libblas.so as Debian.
You need to put symlink replacing libRblas.so (or install R from fedora EPEL to do that for you)
I dont think symlink juggling to emulate Ubuntu alternatives configuration has any effect whatsoever on CentOS or Fedora

[xuyan-piestat]

i have installed binutils install file is pb-binutils224-2.24-1.x86_64.rpm and set its path in /etc/profile echo $PATH /opt/pb/binutils-2.24/bin:/home/data2/daqi/ncl/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/home/data2/daqi/curl-7.51.0/bin:/home/data2/daqi/netcdf-4.1.3/bin:/root/bin

…

------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Fri, Jan 20, 2017 05:43 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Build error: seek OpenBLAS FAQ which tells how to acquire recent binutils on CentOS 6 Then make clean before next build, and make sure to attach full build log, as the missing files are consequence of earlier errors. R configuration: Fedora has no alternatives mechanism for libblas.so as Debian. You need to put symlink replacing libRblas.so (or install R from fedora EPEL to do that for you) I dont think symlink juggling to emulate Ubuntu alternatives configuration has any effect whatsoever on CentOS or Fedora — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[xuyan-piestat]

i am sure i make clean befor next make ,stiil have those error. i am sure i repalce libRblas.so.3 Do i need to replace libRblas.so?

…

------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Fri, Jan 20, 2017 05:43 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Build error: seek OpenBLAS FAQ which tells how to acquire recent binutils on CentOS 6 Then make clean before next build, and make sure to attach full build log, as the missing files are consequence of earlier errors. R configuration: Fedora has no alternatives mechanism for libblas.so as Debian. You need to put symlink replacing libRblas.so (or install R from fedora EPEL to do that for you) I dont think symlink juggling to emulate Ubuntu alternatives configuration has any effect whatsoever on CentOS or Fedora — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[brada4]

Can we get through with successful OpenBLAS build including attaching build log?
I am afraid I can help with drop-in replacement of OpenBLAS on top of vendor RPMs. Your 1km long PATH means it is unfixable.

[xuyan-piestat]

can you give me a binutils installation package,format of rpm or tar for centos and our openblas that can used?

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------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Fri, Jan 20, 2017 06:05 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Can we get through with successful OpenBLAS build including attaching build log? I am afraid I can help with drop-in replacement of OpenBLAS on top of vendor RPMs. Your 1km long PATH means it is unfixable. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[martin-frbg]

Try http://sourceforge.net/projects/slurm-roll/files/addons/6.2.0/rpms/binutils/pb-binutils225-2.25-1.x86_64.rpm (and remember to update your path so tha/opt/pb/binutils-2.25/bin
gets tried first). If compilation still does not work, please upload the log here.

[brada4]

Or better this:
https://github.com/xianyi/OpenBLAS/wiki/faq#binutils

[xuyan-piestat]

now i update my gcc version fro old 4.4.7 to 4.8 , new version is in /usr/local/bin and /usr/local/lib64 , old version is in /usr/bin and /usr/lib64/ , then update-alternatives --install /usr/bin/gcc gcc /usr/local/bin/gcc 101 updatedb echo /usr/local/lib64 make >> /etc/ld.so.conf ldconfig result is : gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.8.0/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ../gcc-4.8.0/configure --enable-checking=release --enable-languages=c,c++,fortran,go --disable-multilib Thread model: posix gcc version 4.8.0 (GCC) then make my openblas ,stiil have errors as : gcc -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=48 -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -w -o linktest linktest.c ../libopenblas_haswellp-r0.2.19.so -L/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.8.0 -L/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.8.0/../../.. -lgfortran -lm -lquadmath -lm -lc && echo OK. /tmp/ccGoZCI8.o: In function `main': linktest.c:(.text.startup+0x2f16): undefined reference to `clagge_' linktest.c:(.text.startup+0x2f1d): undefined reference to `claghe_' linktest.c:(.text.startup+0x2f24): undefined reference to `clagsy_' linktest.c:(.text.startup+0x2f2b): undefined reference to `clahilb_' linktest.c:(.text.startup+0x2f32): undefined reference to `clakf2_' linktest.c:(.text.startup+0x2f39): undefined reference to `clarge_' linktest.c:(.text.startup+0x2f40): undefined reference to `clarnd_' linktest.c:(.text.startup+0x2f47): undefined reference to `claror_' linktest.c:(.text.startup+0x2f4e): undefined reference to `clarot_' linktest.c:(.text.startup+0x2f55): undefined reference to `clatm1_' linktest.c:(.text.startup+0x2f5c): undefined reference to `clatm2_' linktest.c:(.text.startup+0x2f63): undefined reference to `clatm3_' linktest.c:(.text.startup+0x2f6a): undefined reference to `clatm5_' linktest.c:(.text.startup+0x2f71): undefined reference to `clatm6_' linktest.c:(.text.startup+0x2f78): undefined reference to `clatme_' linktest.c:(.text.startup+0x2f7f): undefined reference to `clatmr_' linktest.c:(.text.startup+0x2f86): undefined reference to `clatms_' linktest.c:(.text.startup+0x2f8d): undefined reference to `clatmt_' linktest.c:(.text.startup+0x2ff6): undefined reference to `dlagge_' linktest.c:(.text.startup+0x2ffd): undefined reference to `dlagsy_' linktest.c:(.text.startup+0x3004): undefined reference to `dlahilb_' linktest.c:(.text.startup+0x300b): undefined reference to `dlakf2_' linktest.c:(.text.startup+0x3012): undefined reference to `dlaran_' linktest.c:(.text.startup+0x3019): undefined reference to `dlarge_' linktest.c:(.text.startup+0x3020): undefined reference to `dlarnd_' linktest.c:(.text.startup+0x3027): undefined reference to `dlaror_' linktest.c:(.text.startup+0x302e): undefined reference to `dlarot_' linktest.c:(.text.startup+0x3035): undefined reference to `dlatm1_' linktest.c:(.text.startup+0x303c): undefined reference to `dlatm2_' linktest.c:(.text.startup+0x3043): undefined reference to `dlatm3_' linktest.c:(.text.startup+0x304a): undefined reference to `dlatm5_' linktest.c:(.text.startup+0x3051): undefined reference to `dlatm6_' linktest.c:(.text.startup+0x3058): undefined reference to `dlatm7_' linktest.c:(.text.startup+0x305f): undefined reference to `dlatme_' linktest.c:(.text.startup+0x3066): undefined reference to `dlatmr_' linktest.c:(.text.startup+0x306d): undefined reference to `dlatms_' linktest.c:(.text.startup+0x3074): undefined reference to `dlatmt_' linktest.c:(.text.startup+0x30d6): undefined reference to `slagge_' linktest.c:(.text.startup+0x30dd): undefined reference to `slagsy_' linktest.c:(.text.startup+0x30e4): undefined reference to `slahilb_' linktest.c:(.text.startup+0x30eb): undefined reference to `slakf2_' linktest.c:(.text.startup+0x30f2): undefined reference to `slaran_' linktest.c:(.text.startup+0x30f9): undefined reference to `slarge_' linktest.c:(.text.startup+0x3100): undefined reference to `slarnd_' linktest.c:(.text.startup+0x3107): undefined reference to `slaror_' linktest.c:(.text.startup+0x310e): undefined reference to `slarot_' linktest.c:(.text.startup+0x3115): undefined reference to `slatm1_' linktest.c:(.text.startup+0x311c): undefined reference to `slatm2_' linktest.c:(.text.startup+0x3123): undefined reference to `slatm3_' linktest.c:(.text.startup+0x312a): undefined reference to `slatm5_' linktest.c:(.text.startup+0x3131): undefined reference to `slatm6_' linktest.c:(.text.startup+0x3138): undefined reference to `slatm7_' linktest.c:(.text.startup+0x313f): undefined reference to `slatme_' linktest.c:(.text.startup+0x3146): undefined reference to `slatmr_' linktest.c:(.text.startup+0x314d): undefined reference to `slatms_' linktest.c:(.text.startup+0x3154): undefined reference to `slatmt_' linktest.c:(.text.startup+0x31b6): undefined reference to `zlagge_' linktest.c:(.text.startup+0x31bd): undefined reference to `zlaghe_' linktest.c:(.text.startup+0x31c4): undefined reference to `zlagsy_' linktest.c:(.text.startup+0x31cb): undefined reference to `zlahilb_' linktest.c:(.text.startup+0x31d2): undefined reference to `zlakf2_' linktest.c:(.text.startup+0x31d9): undefined reference to `zlarge_' linktest.c:(.text.startup+0x31e0): undefined reference to `zlarnd_' linktest.c:(.text.startup+0x31e7): undefined reference to `zlaror_' linktest.c:(.text.startup+0x31ee): undefined reference to `zlarot_' linktest.c:(.text.startup+0x31f5): undefined reference to `zlatm1_' linktest.c:(.text.startup+0x31fc): undefined reference to `zlatm2_' linktest.c:(.text.startup+0x3203): undefined reference to `zlatm3_' linktest.c:(.text.startup+0x320a): undefined reference to `zlatm5_' linktest.c:(.text.startup+0x3211): undefined reference to `zlatm6_' linktest.c:(.text.startup+0x3218): undefined reference to `zlatme_' linktest.c:(.text.startup+0x321f): undefined reference to `zlatmr_' linktest.c:(.text.startup+0x3226): undefined reference to `zlatms_' linktest.c:(.text.startup+0x322d): undefined reference to `zlatmt_' collect2: error: ld returned 1 exit status make[1]: *** [../libopenblas_haswellp-r0.2.19.so] Error 1 make[1]: Leaving directory `/home/OpenBLAS-0.2.19/exports' make: *** [shared] Error 2 which library(****.so) i should change from 4.4.7 to 4.8 version? or any suggest?

…

------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Fri, Jan 20, 2017 08:36 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Or better this: https://github.com/xianyi/OpenBLAS/wiki/faq#binutils — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[xuyan-piestat]

can i speak chinese about problem of installation?

…

------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Fri, Jan 20, 2017 08:36 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Or better this: https://github.com/xianyi/OpenBLAS/wiki/faq#binutils — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[martin-frbg]

These are the LAPACK function which are written in FORTRAN, maybe you did not install gcc-gfortran ?

[brada4]

No need to speak Chinese.
OpenBLAS builds perfectly with gcc and gfortran included in
RHEL5 AVX2 via binutils=devtoolset 2.1, min kernel 5U10
6 AVX2 via devtoolst 3+, min kernel 6U3
7 = all supported without any change

Please just choose:
Recipe A

# yum install make gcc gcc-gfortran
$ make NO_AVX2=1

Recipe B

# yum install epel-release
# yum install openblas-devel

Recipe C
is outlined in FAQ

You add too much variables with homebrew build of GCC, it will not be possible to fix any issues.
Please install official software so that we have chance to run into any problems you encounter.

[martin-frbg]

I expect there are enough people here who read Chinese - certainly xianyi at least, and us illiterate westerners can at least try google translate.
Perhaps it would be a good idea to have the FAQ and Installation Guide in the wiki in Chinese (and eventually Arabic) as well ?

[brada4]

Or adhere to simplified english idea in current faq at least...

[xuyan-piestat]

i still failed. i am not new hand of linux .i am sure that i installed gcc-gfortran, two version :4.4.7 and your 4.8 of update.now i switched to your 4.8 version of gcc , and i have no error such as "no ***.so library", i also changed some softlink of /usr/lib64 about libgcc and libgfortran from 4.4.77 to 4.8 . i also executed the command such as : yum install blas blas-devel lapack lapack-devel atlas atlas-devel --nogpgcheck then make FC=gfortran still have errors: linktest.c:(.text.startup+0x76b3): undefined reference to `LAPACKE_zpotrf2' linktest.c:(.text.startup+0x76ba): undefined reference to `LAPACKE_zpotrf2_work' linktest.c:(.text.startup+0x76c1): undefined reference to `LAPACKE_zsytrf_rook' linktest.c:(.text.startup+0x76c8): undefined reference to `LAPACKE_zsytrf_rook_work' linktest.c:(.text.startup+0x76cf): undefined reference to `LAPACKE_zsytrs_rook' linktest.c:(.text.startup+0x76d6): undefined reference to `LAPACKE_zsytrs_rook_work' linktest.c:(.text.startup+0x76dd): undefined reference to `LAPACKE_zuncsd2by1' linktest.c:(.text.startup+0x76e4): undefined reference to `LAPACKE_zuncsd2by1_work' collect2: error: ld returned 1 exit status why? maybe i should set some path for lapack? i locate lapack ,the result is as : /usr/lib64/liblapack.a /usr/lib64/liblapack.so /usr/lib64/liblapack.so.3 /usr/lib64/liblapack.so.3.2.1 /usr/lib64/liblapack_pic.a /usr/lib64/atlas/libclapack.so /usr/lib64/atlas/libclapack.so.3 /usr/lib64/atlas/libclapack.so.3.0 /usr/lib64/atlas/liblapack.a /usr/lib64/atlas/liblapack.so /usr/lib64/atlas/liblapack.so.3 /usr/lib64/atlas/liblapack.so.3.0 /usr/lib64/openblas/liblapack.so.3

…

------------------ Original ------------------ From: "Andrew"<notifications@github.com>; Date: Sun, Jan 22, 2017 08:39 PM To: "xianyi/OpenBLAS"<OpenBLAS@noreply.github.com>; Cc: "xuyan-piestat"<xuyan@piesat.cn>; "Author"<author@noreply.github.com>; Subject: Re: [xianyi/OpenBLAS] openblas centos problem of installation and use(#1070) Or adhere to simplified english idea in current faq at least... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[brada4]

Can you first decide if you want atlas or you want openblas.