[Wien] error in running .machines file

Fri Jun 15 13:05:35 CEST 2018

Gavin has already answered in large part, but let me add a little. You have
two questions/issues which are probably unrelated:
***
1) Is my ssh working?
I suggest that you test this by itself, for instance by running "ssh
othernode" from your head node, and also execute some simple commands that
way, e.g. "ssh othernode ls" and (important) "ssh othernode ldd
$WIENROOT/lapw0_mpi".
***
2) Are the relevant libraries etc on "othernode", and how do I set this up?
This is tricky, and the answer almost certainly is specific to your
cluster. I have been told that there are "security issues" with various
commands that are remotely executed or batch commands. You will need to
find out how to export the relevant environment so lapw0 etc know. At the
moment, even though you are setting up everything on your head node, the
lapw0_mpi running remotely does not have this information.

N.B., sometimes you can change the linking options and use static
compilation, which avoids many or all of the issues in 2).

_____
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu

On Fri, Jun 15, 2018, 4:03 AM venkatesh chandragiri <
venkyphysicsiitm at gmail.com> wrote:

> Dear Prof. Laurence Marks,
>
> thanks for your reply. As pointed in my mail I kept all the variable paths
> to bashrc file as well as in the jobscript file. Also I did the "ldd
> lapw1c_mpi"
>
> the output is ==========
>
> [renwei at ln3 ~/venky/soft/wien2k]$ ldd lapw1c_mpi
>         linux-vdso.so.1 =>  (0x00007ffdad1ea000)
>         libfftw3_mpi.so.3 =>
> /THFS/home/renwei/venky/soft/fftw/lib/libfftw3_mpi.so.3 (0x00002b621871d000)
>         libmkl_scalapack_lp64.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_scalapack_lp64.so
> (0x00002b6218934000)
>         libmkl_blacs_intelmpi_lp64.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so
> (0x00002b621920b000)
>         libfftw3.so.3 =>
> /THFS/home/renwei/venky/soft/fftw/lib/libfftw3.so.3 (0x00002b6219447000)
>         libmkl_intel_lp64.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_lp64.so
> (0x00002b6219753000)
>         libmkl_intel_thread.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_intel_thread.so
> (0x00002b6219ea2000)
>         libmkl_core.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/libmkl_core.so
> (0x00002b621aec1000)
>         libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003cbce00000)
> *        libmpifort.so.12 =>
> /opt/intel/impi/5.0.2.044/intel64/lib/libmpifort.so.12
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__5.0.2.044_intel64_lib_libmpifort.so.12&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=yd5L31TSLK3u3GnBLzDUyNfME-uG53uSknrNwfsE0gA&s=k4MZ4LiJlfMVNw1gDJLrX47uGEksct1IbEUL1dyN5ao&e=>
> (0x00002b621c5d8000)*
>         libmpi.so.12 => /opt/intel/impi/5.0.2.044/intel64/lib/libmpi.so.12
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__5.0.2.044_intel64_lib_libmpi.so.12&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=yd5L31TSLK3u3GnBLzDUyNfME-uG53uSknrNwfsE0gA&s=00PDH74iadjpHyUbYPHfwe2zidZHqw3gbBxiImQPAsk&e=>
> (0x00002b621c861000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x0000003cbca00000)
>         librt.so.1 => /lib64/librt.so.1 (0x0000003cbd600000)
>         libm.so.6 => /lib64/libm.so.6 (0x0000003cbc200000)
>         libiomp5.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64/libiomp5.so
> (0x00002b621cfd5000)
>         libc.so.6 => /lib64/libc.so.6 (0x0000003cbc600000)
>         libgcc_s.so.1 =>
> /THFS/home/sh-hzw2/software/Matlab2014a//sys/os/glnxa64/libgcc_s.so.1
> (0x00002b621d2f1000)
>         libimf.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64/libimf.so
> (0x00002b621d506000)
>         libsvml.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64/libsvml.so
> (0x00002b621d9ca000)
>         libirng.so =>
> /opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64/libirng.so
> (0x00002b621e5c5000)
>         libintlc.so.5 =>
> /opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64/libintlc.so.5
> (0x00002b621e7cc000)
>         /lib64/ld-linux-x86-64.so.2 (0x0000003cbbe00000)
>
> =====================
>
> As I highlighted above *libmpifort.so.*12 has well defined path. do you
> have any comment on this.
>
>
> Further, you are pointed out that "the shared libraries are not present on
> the computer you are connecting to via ssh and/or the path has not been
> exported ". I already copied the key in the
> id_rsa.pub file to authorized_keys file (both are in the same server where
> wien2k installed)  to make the password free ssh.
>
> [renwei at ln3 ~/.ssh]$ ls -la
> total 32
> drwx------  2 renwei renwei  4096 Jun 15 04:10 .
> drwx------ 44 renwei renwei  4096 Jun 15 04:10 ..
> -rw-------  1 renwei renwei  1200 May 19 13:46 authorized_keys
> -rw-------  1 renwei renwei  1675 May 17 13:44 id_rsa
> -rw-r--r--  1 renwei renwei   392 May 17 13:44 id_rsa.pub
> -rw-r--r--  1 renwei renwei 11641 Jun 14 10:45 known_hosts
>
> do I need to change the permission between the authorized_keys &
> id_rsa.pub ...?
>
> thanks
>
> venkatesh
>
>
>
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