`GOMP_4.0' not found

[ignacio quintero]

Hi, 

After updating the INLA version in a linux server (see info below), it crashes and I get the following error. I suspect is because Ubuntu 12.0x is too old?

> dt = data.frame(x = rnorm(10), y = rnorm(10))

> inla(y~x, data=dt)

/usr/local/lib/R/site-library/INLA/bin/linux/64bit/inla: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/local/lib/R/site-library/INLA/bin/linux/64bit/inla)

Error in inla.inlaprogram.has.crashed() :

  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.

  If this does not help, please contact the developers at <he...@r-inla.org>.

> sessionInfo()

R version 3.2.5 (2016-04-14)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu precise (12.04.5 LTS)

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

[1] INLA_0.0-1485844051 Matrix_1.2-1        sp_1.0-13

[4] data.table_1.9.4

loaded via a namespace (and not attached):

 [1] magrittr_1.5    plyr_1.8.2      tools_3.2.5     reshape2_1.4.1

 [5] Rcpp_0.11.3     splines_3.2.5   stringi_0.4-1   grid_3.2.5

 [9] stringr_1.0.0   chron_2.3-45    lattice_0.20-31

Any help would be much appreciated,

i

[ignacio quintero]

Oh, and here is the gcc version:

~$ gcc -v

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)

[Håvard Rue]

On Sun, 2017-04-16 at 08:05 -0700, ignacio quintero wrote:
> I suspect is because Ubuntu
> 12.0x is too old?
>

yes...

you may try the most recent testing version, if that does not work,
with with

library(INLA)
INLA:::inla.dynload.workaround()


to get the static builds.

H

--
Håvard Rue
Department of Mathematical Sciences
Norwegian University of Science and Technology
N-7491 Trondheim, Norway
Voice: +47-7359-3533 URL : http://www.math.ntnu.no/~hrue
Mobile: +47-9260-0021 Email: havar...@math.ntnu.no

R-INLA: www.r-inla.org

[ignacio quintero]

The testing version crashed as well, but the static build did work.

Thank you!

i

[Elizabeth Lee]

Hello -- 

I had been receiving the same "version `GOMP_4.0' not found" error, so I used the line "INLA:::inla.dynload.workaround()" to use the static builds, which did get the model to start to run. Unfortunately, the model now crashes after running for a bit without any additional error message in the R console, even in verbose mode. I am on Ubuntu 14.04 and using INLA version 0.0-1485844051. Are there any additional things related to this GOMP issue that I should check for?

Thank you!

Elizabeth

[INLA help]

On Mon, 2017-05-01 at 15:02 -0700, Elizabeth Lee wrote:
> Hello -- 
> I had been receiving the same "version `GOMP_4.0' not found" error,
> so I used the line "INLA:::inla.dynload.workaround()" to use the
> static builds, which did get the model to start to run.
> Unfortunately, the model now crashes after running for a bit without
> any additional error message in the R console, even in verbose mode.
> I am on Ubuntu 14.04 and using INLA version 0.0-1485844051. Are there
> any additional things related to this GOMP issue that I should check
> for?
>

the ubuntu version is very old...


does this run for a simple model, like

r = inla(y ~ 1, data = data.frame(y=rnorm(10)))

?

--
Håvard Rue
he...@r-inla.org

[Elizabeth Lee]

Yes, it turns out that the simple model will run when I'm accessing the static builds. On the other hand, I tried running the same complex model on a different computer (running Ubuntu 16.04), and the model did not crash.

Elizabeth

--

Elizabeth C. Lee

Ph.D. candidate, Global Infectious Diseases

Georgetown University

https://elizabethclee.wordpress.com/

[INLA help]

On Wed, 2017-05-03 at 14:43 +0000, Elizabeth Lee wrote:
> Yes, it turns out that the simple model will run when I'm accessing
> the static builds. On the other hand, I tried running the same
> complex model on a different computer (running Ubuntu 16.04), and the
> model did not crash.
>

then I suggest to run it there, and request an update on the other
machine to 16.04.

H
--
Håvard Rue
he...@r-inla.org

[Patrick Brown]

I've figured out one of these problems

/lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found

SM upper case

patrick@darjeeling:~$ find /usr/lib/ -iname libsm.so*

/usr/lib/x86_64-linux-gnu/libSM.so.6

/usr/lib/x86_64-linux-gnu/libSM.so.6.0.1

don't understand libgomp though

/usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found 

patrick@darjeeling:~$ find /usr/lib/ -iname libgomp*

/usr/lib/gcc/x86_64-linux-gnu/4.8/libgomp.spec

/usr/lib/gcc/x86_64-linux-gnu/4.8/libgomp.a

/usr/lib/gcc/x86_64-linux-gnu/4.8/libgomp.so

/usr/lib/x86_64-linux-gnu/libgomp.so.1

/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0

p

[INLA help]

On Wed, 2017-05-10 at 06:32 -0700, Patrick Brown wrote:
> I've figured out one of these problems
>

you have an older linux system. either upgrade, or try this

library(INLA)
INLA:::inla.dynload.workaround()


this version has no libR support but I guess you dont use it

--
Håvard Rue
he...@r-inla.org

[Finn Lindgren]

libm, not libsm.

The error message literally says what the problem is; "version XXX not
found", i.e. your library/ies is/are too old.

On my Ubuntu 17.04 machine:

$ strings /lib/x86_64-linux-gnu/libm.so.6 | grep GLIBC
GLIBC_2.2.5
GLIBC_2.4
GLIBC_2.15
GLIBC_2.18
GLIBC_2.23
GLIBC_2.24
GLIBC_PRIVATE

$ strings /usr/lib/gcc/x86_64-linux-gnu/6/libgomp.so|grep GOMP
...
GOMP_1.0
GOMP_2.0
GOMP_3.0
GOMP_4.0
GOMP_4.0.1
GOMP_4.5
...

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--
Finn Lindgren
email: finn.l...@gmail.com

[Patrick Brown]

ah... I'll have to reboot the server to do that... problem for another day.

In my package vignettes I'll always use the static builds, I don't want the package check to fail on old systems.  CRAN frowns on ::: so I've added the following.

if(Sys.info()['sysname'] =='Linux' &

  requireNamespace("INLA")) {   

  INLA::inla.setOption(inla.call = 

      system.file(paste(

          "bin/linux/",          

          ifelse(

            .Machine$sizeof.pointer == 4, 

            "32", "64"),

          'bit/inla.static', sep=''),

        package="INLA")) 

}

Patrick Brown

Department of Statistical Sciences, University of Toronto

pbrown.ca

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[Håvard Rue]

On Wed, 2017-05-10 at 10:01 -0400, Patrick Brown wrote:
> ah... I'll have to reboot the server to do that... problem for
> another day.
>
> In my package vignettes I'll always use the static builds, I don't
> want the package check to fail on old systems.  CRAN frowns on ::: so
> I've added the following.
>
> if(Sys.info()['sysname'] =='Linux' &
>   requireNamespace("INLA")) {   
>   INLA::inla.setOption(inla.call = 
>       system.file(paste(
>           "bin/linux/",          
>           ifelse(
>             .Machine$sizeof.pointer == 4, 
>             "32", "64"),
>           'bit/inla.static', sep=''),
>         package="INLA")) 
> }
>

yes, this is exactly what dynload.workaround() does.

and do the same for 'fmesher' if you use the spde mesh...