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undefined symbol: sgemv_thread_n

9 messages · Dirk Eddelbuettel, Göran Broström

Original
Göran Broström
# 
Hello,

the following is a part of a question asked on R-help. I realized that 
it is better suited for asking here. Apologies for the cross-posting!

I'm on Ubuntu artful, and upgraded with 'apt'. Then

----------------------------------------------------------------
goran at M6800:~/src/R-3.4.3$ /usr/bin/R
/usr/lib/R/bin/exec/R: symbol lookup error: 
/usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: sgemv_thread_n
----------------------------------------------------------------

Never seen this before. What can I do?

G?ran Brostr?m
Dirk Eddelbuettel
#
On 1 December 2017 at 19:55, G?ran Brostr?m wrote:
| Hello,
| 
| the following is a part of a question asked on R-help. I realized that 
| it is better suited for asking here. Apologies for the cross-posting!
| 
| I'm on Ubuntu artful, and upgraded with 'apt'. Then
| 
| ----------------------------------------------------------------
| goran at M6800:~/src/R-3.4.3$ /usr/bin/R
| /usr/lib/R/bin/exec/R: symbol lookup error: 
| /usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: sgemv_thread_n
| ----------------------------------------------------------------
| 
| Never seen this before. What can I do?

At home:

edd at bud:~$ COLUMNS=70 dpkg -l | grep blas
ii  libblas-common 3.7.0-1      amd64        Dependency package for all BLAS i
ii  libblas-dev    3.7.0-1      amd64        Basic Linear Algebra Subroutines 
ii  libblas3       3.7.0-1      amd64        Basic Linear Algebra Reference im
ii  libopenblas-ba 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
edd at bud:~$

At work:
........ at .....:~$ COLUMNS=70 dpkg -l | grep blas
ii  libblas-common 3.7.0-1      amd64        Dependency package for all BLAS i
ii  libblas-dev    3.7.0-1      amd64        Basic Linear Algebra Subroutines 
ii  libblas3       3.7.0-1      amd64        Basic Linear Algebra Reference im
ii  libcublas8.0:a 8.0.44-3     amd64        NVIDIA cuBLAS Library
ii  libnvblas8.0:a 8.0.44-3     amd64        NVBLAS runtime library
ii  libopenblas-ba 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
ii  libopenblas-de 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
........ at .....:~$ 

In other words, I tend to use standard blas or openblas or atlas (but
seemingly less often).  Both are 17.04, but that doesn't matter as they both
have been updated regularly over the years.

You must have gotten out of whack between what compiled R, and what runs it.
Did you by chance compile R 3.4.3 locally?

Dirk
Dirk Eddelbuettel
#
On 1 December 2017 at 13:24, Dirk Eddelbuettel wrote:
|
| On 1 December 2017 at 19:55, G?ran Brostr?m wrote:
| | Hello,
| | 
| | the following is a part of a question asked on R-help. I realized that 
| | it is better suited for asking here. Apologies for the cross-posting!
| | 
| | I'm on Ubuntu artful, and upgraded with 'apt'. Then
| | 
| | ----------------------------------------------------------------
| | goran at M6800:~/src/R-3.4.3$ /usr/bin/R
| | /usr/lib/R/bin/exec/R: symbol lookup error: 
| | /usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: sgemv_thread_n
| | ----------------------------------------------------------------
| | 
| | Never seen this before. What can I do?
| 
| At home:
| 
| edd at bud:~$ COLUMNS=70 dpkg -l | grep blas
| ii  libblas-common 3.7.0-1      amd64        Dependency package for all BLAS i
| ii  libblas-dev    3.7.0-1      amd64        Basic Linear Algebra Subroutines 
| ii  libblas3       3.7.0-1      amd64        Basic Linear Algebra Reference im
| ii  libopenblas-ba 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
| edd at bud:~$
| 
| At work:
| ........ at .....:~$ COLUMNS=70 dpkg -l | grep blas
| ii  libblas-common 3.7.0-1      amd64        Dependency package for all BLAS i
| ii  libblas-dev    3.7.0-1      amd64        Basic Linear Algebra Subroutines 
| ii  libblas3       3.7.0-1      amd64        Basic Linear Algebra Reference im
| ii  libcublas8.0:a 8.0.44-3     amd64        NVIDIA cuBLAS Library
| ii  libnvblas8.0:a 8.0.44-3     amd64        NVBLAS runtime library
| ii  libopenblas-ba 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
| ii  libopenblas-de 0.2.19-2     amd64        Optimized BLAS (linear algebra) l
| ........ at .....:~$ 
| 
| In other words, I tend to use standard blas or openblas or atlas (but
| seemingly less often).  Both are 17.04, but that doesn't matter as they both
| have been updated regularly over the years.
| 
| You must have gotten out of whack between what compiled R, and what runs it.
| Did you by chance compile R 3.4.3 locally?

And R 3.4.3 is now as a .deb on the CRAN mirrors and starts as expected as
well.  So your troubles may well be home-grown...

Dirk
Göran Broström
# 
Den 2017-12-01 kl. 20:24, skrev Dirk Eddelbuettel:
Yes, first I installed R-3.4.3 from source and it started OK, but when I 
tried

 > library(eha)

I got the error above.

So I installed by apt, and then I got the above.

This is what I always have done, installing both from source and the 
ubuntu versions via 'apt upgrade', and it has always worked without 
problems. What has changed now? And how can I get out of this?

G?ran
Dirk Eddelbuettel
#
On 1 December 2017 at 21:12, G?ran Brostr?m wrote:
| Yes, first I installed R-3.4.3 from source and it started OK, but when I 
| tried
| 
|  > library(eha)
| 
| I got the error above.

At that point I suggest to reinstall eha, and/or do 'ldd' on its shared
library to find out what it thinks it is pointing to.  The 'threaded gemv'
must be coming from somewhere.
 
| So I installed by apt, and then I got the above.

You may now have several R's on your system so you need to check your path.
Remember /usr/local generally wins so even if you have a self-compiled R and
a packaged on 'R' will probably get you /usr/local/bin/R.
 
| This is what I always have done, installing both from source and the 
| ubuntu versions via 'apt upgrade', and it has always worked without 
| problems. What has changed now? And how can I get out of this?

We cannot tell. This is somewhat incomplete information. It appears to be
related to your computer.

You may be tired of me saying 'Docker' but it gives you a clean room, akin to
installing on a fresh empty machine.  Useful for debugging.

Dirk
Göran Broström
# 
Dirk,

thanks for your help. At work I have (ubuntu 16.04):

ii  libblas-common 3.6.0-2ubuntu2  amd64        Dependency package for 
all BLAS implementations
ii  libblas-dev    3.6.0-2ubuntu2  amd64        Basic Linear Algebra 
Subroutines 3, static library
ii  libblas3       3.6.0-2ubuntu2  amd64        Basic Linear Algebra 
Reference implementations, shared library

and everything works before and after upgrading (/usr/bin/R). However, 
at home (ubuntu 17.10):

goran at M6800:~$ dpkg -l | grep blas
ii  libblas-dev:amd64 3.7.1-3ubuntu2   amd64        Basic Linear Algebra 
Subroutines 3, static library
ii  libblas3:amd64    3.7.1-3ubuntu2   amd64        Basic Linear Algebra 
Reference implementations, shared library
ii  libopenblas-base:amd64  0.2.20+ds-4  amd64        Optimized BLAS 
(linear algebra) library (shared library)

and it worked before upgrade but not after. Seems to be missing 
'libblas-common'. So I try to install:

goran at M6800:~$ sudo apt install libblas-common
[sudo] password for goran:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libblas-common

So there is no such package in 17.10, but I have it in 16.04. What can 
be the replacement? Maybe I should downgrade to R-3.4.2, which works, 
but it doesn't feel right.

G?ran
On 2017-12-01 21:12, G?ran Brostr?m wrote:
Dirk Eddelbuettel
# 
Hi there,
On 1 December 2017 at 23:24, G?ran Brostr?m wrote:
| Dirk,
| 
| thanks for your help. At work I have (ubuntu 16.04):
| 
| ii  libblas-common 3.6.0-2ubuntu2  amd64        Dependency package for 
| all BLAS implementations
| ii  libblas-dev    3.6.0-2ubuntu2  amd64        Basic Linear Algebra 
| Subroutines 3, static library
| ii  libblas3       3.6.0-2ubuntu2  amd64        Basic Linear Algebra 
| Reference implementations, shared library
| 
| and everything works before and after upgrading (/usr/bin/R). However, 
| at home (ubuntu 17.10):
| 
| goran at M6800:~$ dpkg -l | grep blas
| ii  libblas-dev:amd64 3.7.1-3ubuntu2   amd64        Basic Linear Algebra 
| Subroutines 3, static library
| ii  libblas3:amd64    3.7.1-3ubuntu2   amd64        Basic Linear Algebra 
| Reference implementations, shared library
| ii  libopenblas-base:amd64  0.2.20+ds-4  amd64        Optimized BLAS 
| (linear algebra) library (shared library)
| 
| and it worked before upgrade but not after. Seems to be missing 
| 'libblas-common'.

Maybe. Maybe not. Did you check packages.ubuntu.com (or another source) to
see if it still exists?  Per
https://packages.ubuntu.com/search?keywords=libblas-common it is only listed
for xenial (16.04) and zesty (17.04), not your 17.10.

| So I try to install:
| 
| goran at M6800:~$ sudo apt install libblas-common
| [sudo] password for goran:
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| E: Unable to locate package libblas-common
| 
| So there is no such package in 17.10, but I have it in 16.04. What can 
| be the replacement? Maybe I should downgrade to R-3.4.2, which works, 
| but it doesn't feel right.

No that would not be right.

To recap: you have an issue on 17.10 only, and the R is self-built or the one
installable as binary via CRAN?

Dirk
Göran Broström
#
On 2017-12-01 23:33, Dirk Eddelbuettel wrote:
Yes, that is what I found.
The binary via CRAN. I had both versions a few hours ago, but I 
uninstalled both ('dpkg --purge r-base' and 'sudo make uninstall' + 
removing everything under /usr/local/lib/R/'. Then I installed r-base 
('sudo apt install r-base') and the error message is the same.

G?ran
Göran Broström
# 
Hi,

I removed openblas:

goran at M6800:~$ sudo dpkg --purge libopenblas-dev

and

goran at M6800:~$ sudo dpkg --purge libopenblas-base

which left me with

goran at M6800:~$ dpkg -l | grep blas
pi  libblas-dev:amd64 3.7.1-3ubuntu2  amd64        Basic Linear Algebra 
Subroutines 3, static library
ii  libblas3:amd64  3.7.1-3ubuntu2 amd64        Basic Linear Algebra 
Reference implementations, shared library

And now everything just works.

G?ran
On 2017-12-01 23:33, Dirk Eddelbuettel wrote: