Problem in installation of parallel-3.1.2.tar.gz, undefined symbol: gnutls_srp_base64_decode_alloc

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Problem in installation of parallel-3.1.2.tar.gz, undefined symbol: gnutls_srp_base64_decode_alloc

Ivan Spisso
Hi,

I am trying to install octave in HPC cluster, MArconi A1 bdw based cluser

https://wiki.u-gov.it/confluence/display/SCAIUS/UG3.1%3A+MARCONI+UserGuide

I have installed octave 4.2.2 with gnutls/

[ispisso0@r000u08l03 ~]$ module li
Currently Loaded Modulefiles:
  1) profile/global
  2) autoload
  3) profile/advanced
  4) jdk/1.8.0_111
  5) gnu/6.1.0
  6) zlib/1.2.8--gnu--6.1.0
  7) blas/3.6.0--gnu--6.1.0
  8) lapack/3.6.1--gnu--6.1.0
  9) szip/2.1--gnu--6.1.0
10) hdf5/1.8.17--gnu--6.1.0
11) openmpi/1-10.3--gnu--6.1.0
12) fftw/3.3.4--openmpi--1-10.3--gnu--6.1.0
13) libnettle/3.4--gnu--6.1.0
14) gmp/6.1.1--gnu--6.1.0
15) gnutls/3.6.2--gnu--6.1.0
16) octave/4.2.2

I have tried to install struct-1.0.14.tar.gz + parallel-3.1.2.tar.gz package

Everything seems fine, except at the end when the parallel package has
to installed.

The installation fials with

/marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
failed to load:
/marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
undefined symbol: gnutls_srp_base64_decode_alloc
error: called from

Looking to the installation path

Looking at the installation path

/cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/

[ispisso0@r000u08l03 ~]$ ls
/cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode*
../man3/gnutls_srp_base64_decode2.3
../man3/gnutls_srp_base64_decode.3

The API

/man3/gnutls_srp_base64_decode_alloc.3

is missing, but it seems that the API decode_alloc.3 has been replaced
in the version 3.4.10 by _decode2.3

http://mail-index.netbsd.org/pkgsrc-wip-changes/2016/03/23/msg002234.html

man/man3/gnutls_srp_base64_decode.3
-man/man3/gnutls_srp_base64_decode_alloc.3
+man/man3/gnutls_srp_base64_decode2.3


Something wrong in my configuration/installation?

Regards

Ivan




--
Ivan Spisso, Ph.D.
HPC consultant for academic and industrial CFD applications
SuperComputing Applications and Innovation (SCAI) Department, CINECA
via Magnanelli 6/3, 40133  Casalecchio di Reno, Bologna (Italy)
ph.  (+39) 051 6171 445
web: www.hpc.cineca.it
e-mail: [hidden email]
skype: ivanspisso
hangout: [hidden email]



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Re: Problem in installation of parallel-3.1.2.tar.gz, undefined symbol: gnutls_srp_base64_decode_alloc

Olaf Till-2
On Fri, May 25, 2018 at 05:26:14PM +0200, Ivan Spisso wrote:

> ...
> /marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
> failed to load: /marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
> undefined symbol: gnutls_srp_base64_decode_alloc
> error: called from
>
> Looking to the installation path
>
> Looking at the installation path
>
> /cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/
>
> [ispisso0@r000u08l03 ~]$ ls /cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode*
> ../man3/gnutls_srp_base64_decode2.3
> ../man3/gnutls_srp_base64_decode.3
>
> The API
>
> /man3/gnutls_srp_base64_decode_alloc.3
>
> is missing, but it seems that the API decode_alloc.3 has been replaced in
> the version 3.4.10 by _decode2.3
Indeed gnutls_srp_base64_decode_alloc seems to be gone in gnutls
3.6.2. I wasn't aware of this backwards-incompatibility of gnutls, in
my version 3.5.8 the symbol is still in.

This has to be fixed in the parallel package. Maybe you can submit a
bug report so it won't be forgotten.

Maybe you don't need gnutls -- if you don't use an unsafe
cluster. Unfortunately, there is currently no way to explicitly
disable gnutls while building the package. But it will be disabled
automatically if no gnutls is found during package building.

Olaf

--
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Re: Problem in installation of parallel-3.1.2.tar.gz, undefined symbol: gnutls_srp_base64_decode_alloc

Ivan Spisso

Dear Olaf,

thanks for your answer.


Il 25/05/2018 21:43, Olaf Till ha scritto:
On Fri, May 25, 2018 at 05:26:14PM +0200, Ivan Spisso wrote:
...
/marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
failed to load: /marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct:
undefined symbol: gnutls_srp_base64_decode_alloc
error: called from

Looking to the installation path

Looking at the installation path

/cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/

[ispisso0@r000u08l03 ~]$ ls /cineca/prod/opt/libraries/gnutls/3.6.2/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode*
../man3/gnutls_srp_base64_decode2.3
../man3/gnutls_srp_base64_decode.3

The API

/man3/gnutls_srp_base64_decode_alloc.3

is missing, but it seems that the API decode_alloc.3 has been replaced in
the version 3.4.10 by _decode2.3
Indeed gnutls_srp_base64_decode_alloc seems to be gone in gnutls
3.6.2. I wasn't aware of this backwards-incompatibility of gnutls, in
my version 3.5.8 the symbol is still in.
I have installed the gnutls/3.5.8 in our cluster, and still same issue

make: Leaving directory `/tmp/oct-GanupR/parallel-3.1.2/src'
copyfile /tmp/oct-GanupR/parallel-3.1.2/src/__netcellfun_guardfun__.m /tmp/oct-GanupR/parallel-3.1.2/src/__pserver_exit__.m /tmp/oct-Ginstall_vars.m /tmp/oct-GanupR/parallel-3.1.2/src/netarrayfun.m /tmp/oct-GanupR/parallel-3.1.2/src/netcellfun.m /tmp/oct-GanupR/parallp/oct-GanupR/parallel-3.1.2/src/scloseall.m /tmp/oct-GanupR/parallel-3.1.2/src/server.m/tmp/oct-GanupR/parallel-3.1.2/inst
copyfile /tmp/oct-GanupR/parallel-3.1.2/src/__exit__.oct /tmp/oct-GanupR/parallel-3.1.2/src/__visglobal__.oct /tmp/oct-GanupR/parallel/oct-GanupR/parallel-3.1.2/src/fsave.oct /tmp/oct-GanupR/parallel-3.1.2/src/parallel_generate_srp_data.oct /tmp/oct-GanupR/parallel-3.e.oct /tmp/oct-GanupR/parallel-3.1.2/src/select.oct /tmp/oct-GanupR/parallel-3.1.2/inst/x86_64-pc-linux-gnu-api-v51
/marconi/home/userinternal/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct: failed to load: l/ispisso0/octave/parallel-3.1.2/x86_64-pc-linux-gnu-api-v51/parallel_generate_srp_data.oct: undefined symbol: gnutls_srp_base64_decod
error: called from
    doc_cache_create>create_cache at line 109 column 18
    gen_doc_cache_in_dir>@<anonymous> at line 143 column 16
    doc_cache_create>gen_doc_cache_in_dir at line 144 column 9
    doc_cache_create at line 55 column 12
    install>generate_lookfor_cache at line 797 column 5
    install at line 231 column 7
    pkg at line 394 column 9

 Unfortunately, looking at the installation path,

 ls /cineca/prod/opt/libraries/gnutls/3.5.8/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode*
/cineca/prod/opt/libraries/gnutls/3.5.8/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode2.3
/cineca/prod/opt/libraries/gnutls/3.5.8/gnu--6.1.0/share/man/man3/gnutls_srp_base64_decode.3


there is no

gnutls_srp_base64_decode_alloc.3

This has to be fixed in the parallel package. Maybe you can submit a
bug report so it won't be forgotten.
Yes, I am going to open a bug report

Maybe you don't need gnutls -- if you don't use an unsafe
cluster. Unfortunately, there is currently no way to explicitly
disable gnutls while building the package. But it will be disabled
automatically if no gnutls is found during package building.
If I have understood, I can try to compile octave without gnutls in the pre-requisites, and it should work?

Olaf

Thanks

Ivan
-- 
Ivan Spisso, Ph.D.
HPC consultant for academic and industrial CFD applications
SuperComputing Applications and Innovation (SCAI) Department, CINECA
via Magnanelli 6/3, 40133  Casalecchio di Reno, Bologna (Italy)
ph.  (+39) 051 6171 445
web: www.hpc.cineca.it
e-mail: [hidden email]
skype: ivanspisso
hangout: [hidden email]