openblas centos problem of installation and use #1070
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Build error: R configuration: |
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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
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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
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Can we get through with successful OpenBLAS build including attaching build log? |
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can you give me a binutils installation package,format of rpm or tar for centos and our openblas that can used?
…------------------ 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.
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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 |
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Or better this: |
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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
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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
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These are the LAPACK function which are written in FORTRAN, maybe you did not install gcc-gfortran ? |
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No need to speak Chinese. Please just choose: Recipe B Recipe C You add too much variables with homebrew build of GCC, it will not be possible to fix any issues. |
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I expect there are enough people here who read Chinese - certainly xianyi at least, and us illiterate westerners can at least try google translate. |
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Or adhere to simplified english idea in current faq at least... |
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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...
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Can you first decide if you want atlas or you want openblas. |
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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 tozlatmr_'linktest.c:(.text+0x3226): undefined reference to
zlatms_' linktest.c:(.text+0x322d): undefined reference tozlatmt_'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)
both almost have no difference . I donot know why.
anyone tell me which step is wrong in my process.
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