Hi, All

We've installed MEEP on our SunFire V890 based cluster. The software
(MEEP) ain't working properly and that's the main reason of posting to
this mailing list. Perhaps we could get some guidance on this forum on how
to resolve the issue.

-bash-3.00$ uname -a
SunOS indus1 5.10 Generic_118833-36 sun4u sparc SUNW,Sun-Fire-V890

Contents of the email
=====================

a) Three tests that show MEEP failing
b) Installation procedure
c) Environment Information
d) Contents of logs.tar.gz - you can download it from
http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz


a) Three tests that show MEEP failing
=====================================

Basically, three "tests" that suggest some problem with installation.
These include, MEEP's "make check", $MEEP_HOME/examples/ring.ctl
simulation, and $MEEP_HOME/examples/ring.ctl.

1. MEEP's "make check" fails.
[ .. the output is attached .. ]

2. Running $MEEP_HOME/examples/ring.ctl simulation fails:

_________________________________________________

bash-3.00$ mpirun -np 1 ~/install/meep/bin/meep-mpi ring.ctl
Using MPI version 2.0, 1 processes
-----------
Initializing structure...
Working in 2D dimensions.
     cylinder, center = (0,0,0)
          radius 2, height 1e+20, axis (0, 0, 1)
          dielectric constant epsilon = 11.56
     cylinder, center = (0,0,0)
          radius 1, height 1e+20, axis (0, 0, 1)
          dielectric constant epsilon = 1
Halving computational cell along direction y
time for set_epsilon = 0.177334 s
-----------
creating output file "./ring-eps-000000.00.h5"...
Meep progress: 0.05/300.0 = 0.0% done in 6.6s, 39728.3s to go
harminv0:, frequency, imag. freq., Q, |amp|, amplitude, error
harminv: failure on line 853 of harminv.c: argument out of range in
harminv_get_amplitude

Some deprecated features have been used.  Set the environment
variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
program to get more information.  Set it to "no" to suppress
this message.
_________________________________________________

3. Running $MEEP_HOME/examples/ring.ctl simulation fails:
_________________________________________________

bash-3.00$ mpirun -np 1 ~/install/meep/bin/meep-mpi bend-flux.ctl
Using MPI version 2.0, 1 processes
-----------
Initializing structure...
Working in 2D dimensions.
     block, center = (-2,-11.5,0)
          size (12,1,1e+20)
          axes (1,0,0), (0,1,0), (0,0,1)
          dielectric constant epsilon = 12
     block, center = (3.5,2,0)
          size (1,28,1e+20)
          axes (1,0,0), (0,1,0), (0,0,1)
          dielectric constant epsilon = 12
time for set_epsilon = 0.443259 s
-----------
ADIOI_NFS_OPEN (line 55): **filenoexist
./bend-flux-refl-flux.h5ADIOI_NFS_OPEN (line 55): **filenoexist
./bend-flux-refl-flux.h5MPI_FILE_CLOSE (line 51): **iobadfh
HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 MPI-process 0.
Back trace follows.
  #000: H5F.c line 2048 in H5Fopen(): unable to open file
    major(04): File interface
    minor(17): Unable to open file
  #001: H5F.c line 1725 in H5F_open(): unable to open file
    major(04): File interface
    minor(17): Unable to open file
  #002: H5FD.c line 1044 in H5FD_open(): open failed
    major(22): Virtual File Layer
    minor(29): Unable to initialize object
  #003: H5FDmpio.c line 798 in H5FD_mpio_open(): MPI_File_open failed
    major(03): Internal HDF5 error
    minor(78): Some MPI function failed
  #004: H5FDmpio.c line 798 in H5FD_mpio_open(): MPI_ERR_NO_SUCH_FILE: no
such file or directory
    major(03): Internal HDF5 error
    minor(79): MPI Error String
meep: error on line 243 of h5file.cpp: error opening HDF5 input file
[indus1:11331] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1

Some deprecated features have been used.  Set the environment
variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
program to get more information.  Set it to "no" to suppress
this message.
_________________________________________________

b) Installation procedure
=========================

It turns out that Sun Studio installation contains BLAS and LAPACK. These
are contained in /opt/SUNWspro directory.

Install Harminv
---------------

These instructions are valid for indus1 (the head node of our SunFire V890
cluster).

Install harminv with the following commands:

./configure --with-blas=/opt/SUNWspro/lib/libsunperf.so
--with-lapack=/opt/SUNWspro/lib/libsunperf.so
--prefix=/home/aamir/install/harminv

make ; make install

Install Guile
-------------

Guile is install through pkg-get install. The version of guile is 1.6.7.
It is installed in /opt/csw/bin and /opt/csw/lib

Install libctl
--------------

Install libctl with the following commands:

./configure --prefix=/home/aamir/install/libctl

make ; make install

Install hdf5
------------

Install hdf5 with the following commands:

./configure --prefix=/home/aamir/install/hdf5 --enable-parallel

make ; make install

Install MPI
-----------

Sun HPC Cluster Toolkit 7.0 now contains a customized version od Open MPI.
The version 6.0 had Sun MPI.

This toolkit is installed in /opt/SUNWhpc/HPC7.0 and I'm using the MPI
library inside this toolkit.

Install Meep
------------

Install meep with the following commands:

./configure --prefix=/home/aamir/install/meep --with-mpi
--with-libctl=/home/aamir/install/libctl/share/libctl
--with-blas=/opt/SUNWspro/lib/libsunperf.so
--with-lapack=/opt/SUNWspro/lib/libsunperf.so

make ; make install

c) Environment Information
==========================

-bash-3.00$ echo $LD_LIBRARY_PATH
/home/aamir/install/meep/lib:/home/aamir/install/hdf5/lib:/opt/SUNWhpc/HPC7.0/lib:/home/aamir/install/harminv/lib:/opt/csw/lib:/home/aamir/install/libctl/lib

-bash-3.00$ echo $PATH
/home/aamir/install/harminv/bin:/opt/SUNWspro/bin:/opt/csw/gcc3/bin:/usr/bin:/opt/csw/bin:/opt/SUNWspro/bin:/usr/sfw/bin:/usr/cluster/bin:/usr/ccs/bin:/usr/sbin:/opt/SUNWexplo/bin:/opt/SUNWrtvc/bin:/opt/SUNWsneep/bin:/bin:/usr/openwin/bin:/usr/ucb:/usr/sfw/bin:/opt/csw/bin:/usr/bin:/opt/SUNWhpc/HPC7.0/bin:/home/aamir/install/hdf5/bin:/home/aamir/install/libctl/bin:/home/aamir/install/meep/bin
-bash-3.00$ echo $CPPFLAGS
-I/home/aamir/install/harminv/include -I/opt/csw/include
-I/home/aamir/install/libctl/include -I/opt/SUNWhpc/HPC7.0/include
-I/home/aamir/install/hdf5/include -I/home/aamir/install/meep/include

-bash-3.00$ echo $LDFLAGS
-L/home/aamir/install/harminv/lib -L/opt/csw/lib
-L/home/aamir/install/libctl/lib -L/opt/SUNWhpc/HPC7.0/lib
-L/home/aamir/install/hdf5/lib -L/home/aamir/install/meep/lib

-bash-3.00$ echo $PKG_CONFIG_PATH
:/home/aamir/install/harminv/lib/pkgconfig

d) Contents of logs.tar.gz (http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz)
======================================

(http://hpc.niit.edu.pk/~aamir/res/logs.tar.gz)

Output of bend-flux example  --> bendflux_example.log
Output of MEEP's make        --> make.log
Output of ring example       --> ring_example.log
Output of MEEP's ./configure --> config.log
Output of MEEP's make all    --> make_all.log
Output of HDF5 make check    --> hdf5_makecheck.log
Output of MEEP's make check  --> make_check.log

--Aamir


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


_______________________________________________
meep-discuss mailing list
meep-discuss@ab-initio.mit.edu
http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss

Reply via email to