Hi,

Can you give more info about the compilation steps, I just recompiled it (using the internal stuff except for fftw) and was able to run an example (output below). Did I miss something ?

I recompiled / ran on a Platform OCS 5 cluster (based on RHEL 5), with IB support (OFED)

Partial ompi_info :

Open MPI: 1.2.6

Open MPI SVN revision: r17946

Open RTE: 1.2.6

Open RTE SVN revision: r17946

OPAL: 1.2.6

OPAL SVN revision: r17946

Prefix: /home/mbozzore/openmpi

Configured architecture: x86_64-unknown-linux-gnu

Configured by: mbozzore

Configured on: Mon Aug 11 00:29:15 EDT 2008

Configure host: tyan04.lsf.platform.com

Built by: mbozzore

Built on: Mon Aug 11 00:33:54 EDT 2008

Built host: tyan04.lsf.platform.com

C bindings: yes

C++ bindings: yes

Fortran77 bindings: yes (all)

Fortran90 bindings: yes

Fortran90 bindings size: small

C compiler: gcc

C compiler absolute: /usr/bin/gcc

C++ compiler: g++

C++ compiler absolute: /usr/bin/g++

Fortran77 compiler: gfortran

Fortran77 compiler abs: /usr/bin/gfortran

Fortran90 compiler: gfortran

Fortran90 compiler abs: /usr/bin/gfortran

[mbozzore@tyan04 tests]$ mpirun -np 4 --machinefile ./hosts -x LD_LIBRARY_PATH --mca btl openib,self ../bin/pw.x < scf.in

Program PWSCF v.4.0.1 starts ...

Today is 15Aug2008 at 14:51:18

Parallel version (MPI)

Number of processors in use: 4

R & G space division: proc/pool = 4

For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW

Current dimensions of program pwscf are:

Max number of different atomic species (ntypx) = 10

Max number of k-points (npk) = 40000

Max angular momentum in pseudopotentials (lmaxx) = 3

Iterative solution of the eigenvalue problem

a parallel distributed memory algorithm will be used,

eigenstates matrixes will be distributed block like on

ortho sub-group = 2* 2 procs

Planes per process (thick) : nr3 = 16 npp = 4 ncplane = 256

Proc/ planes cols G planes cols G columns G

Pool (dense grid) (smooth grid) (wavefct grid)

1 4 41 366 4 41 366 13 70

2 4 41 366 4 41 366 14 71

3 4 40 362 4 40 362 14 71

4 4 41 365 4 41 365 14 71

tot 16 163 1459 16 163 1459 55 283

bravais-lattice index = 2

lattice parameter (a_0) = 10.2000 a.u.

unit-cell volume = 265.3020 (a.u.)^3

number of atoms/cell = 2

number of atomic types = 1

number of electrons = 8.00

number of Kohn-Sham states= 4

kinetic-energy cutoff = 12.0000 Ry

charge density cutoff = 48.0000 Ry

convergence threshold = 1.0E-06

mixing beta = 0.7000

number of iterations used = 8 plain mixing

Exchange-correlation = SLA PZ NOGX NOGC (1100)

celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000

celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

crystal axes: (cart. coord. in units of a_0)

a(1) = ( -0.500000 0.000000 0.500000 )

a(2) = ( 0.000000 0.500000 0.500000 )

a(3) = ( -0.500000 0.500000 0.000000 )

reciprocal axes: (cart. coord. in units 2 pi/a_0)

b(1) = ( -1.000000 -1.000000 1.000000 )

b(2) = ( 1.000000 1.000000 1.000000 )

b(3) = ( -1.000000 1.000000 -1.000000 )

PseudoPot. # 1 for Si read from file Si.vbc.UPF

Pseudo is Norm-conserving, Zval = 4.0

Generated by new atomic code, or converted to UPF format

Using radial grid of 431 points, 2 beta functions with:

l(1) = 0

l(2) = 1

atomic species valence mass pseudopotential

Si 4.00 28.08600 Si( 1.00)

48 Sym.Ops. (with inversion)

Cartesian axes

site n. atom positions (a_0 units)

1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )

2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 )

number of k points= 2

cart. coord. in units 2pi/a_0

k( 1) = ( 0.2500000 0.2500000 0.2500000), wk = 0.5000000

k( 2) = ( 0.2500000 0.2500000 0.7500000), wk = 1.5000000

G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, 16)

Largest allocated arrays est. size (Mb) dimensions

Kohn-Sham Wavefunctions 0.00 Mb ( 51, 4)

NL pseudopotentials 0.01 Mb ( 51, 8)

Each V/rho on FFT grid 0.02 Mb ( 1024)

Each G-vector array 0.00 Mb ( 366)

G-vector shells 0.00 Mb ( 42)

Largest temporary arrays est. size (Mb) dimensions

Auxiliary wavefunctions 0.01 Mb ( 51, 16)

Each subspace H/S matrix 0.00 Mb ( 16, 16)

Each <psi_i|beta_j> matrix 0.00 Mb ( 8, 4)

Arrays for rho mixing 0.13 Mb ( 1024, 8)

Initial potential from superposition of free atoms

starting charge 7.99901, renormalised to 8.00000

Starting wfc are 8 atomic wfcs

total cpu time spent up to now is 0.10 secs

per-process dynamical memory: 21.9 Mb

Self-consistent Calculation

iteration # 1 ecut= 12.00 Ry beta=0.70

Davidson diagonalization with overlap

ethr = 1.00E-02, avg # of iterations = 2.0

Threshold (ethr) on eigenvalues was too large:

Diagonalizing with lowered threshold

Davidson diagonalization with overlap

ethr = 7.93E-04, avg # of iterations = 1.0

total cpu time spent up to now is 0.13 secs

total energy = -15.79103983 Ry

Harris-Foulkes estimate = -15.81239602 Ry

estimated scf accuracy < 0.06375741 Ry

iteration # 2 ecut= 12.00 Ry beta=0.70

Davidson diagonalization with overlap

ethr = 7.97E-04, avg # of iterations = 1.0

total cpu time spent up to now is 0.15 secs

total energy = -15.79409517 Ry

Harris-Foulkes estimate = -15.79442220 Ry

estimated scf accuracy < 0.00230261 Ry

iteration # 3 ecut= 12.00 Ry beta=0.70

Davidson diagonalization with overlap

ethr = 2.88E-05, avg # of iterations = 2.0

total cpu time spent up to now is 0.17 secs

total energy = -15.79447768 Ry

Harris-Foulkes estimate = -15.79450039 Ry

estimated scf accuracy < 0.00006345 Ry

iteration # 4 ecut= 12.00 Ry beta=0.70

Davidson diagonalization with overlap

ethr = 7.93E-07, avg # of iterations = 2.0

total cpu time spent up to now is 0.19 secs

total energy = -15.79449472 Ry

Harris-Foulkes estimate = -15.79449644 Ry

estimated scf accuracy < 0.00000455 Ry

iteration # 5 ecut= 12.00 Ry beta=0.70

Davidson diagonalization with overlap

ethr = 5.69E-08, avg # of iterations = 2.5

total cpu time spent up to now is 0.21 secs

End of self-consistent calculation

k = 0.2500 0.2500 0.2500 ( 180 PWs) bands (ev):

-4.8701 2.3792 5.5371 5.5371

k = 0.2500 0.2500 0.7500 ( 186 PWs) bands (ev):

-2.9165 -0.0653 2.6795 4.0355

! total energy = -15.79449556 Ry

Harris-Foulkes estimate = -15.79449558 Ry

estimated scf accuracy < 0.00000005 Ry

The total energy is the sum of the following terms:

one-electron contribution = 4.83378726 Ry

hartree contribution = 1.08428951 Ry

xc contribution = -4.81281375 Ry

ewald contribution = -16.89975858 Ry

convergence has been achieved in 5 iterations

entering subroutine stress ...

total stress (Ry/bohr**3) (kbar) P= -30.30

-0.00020597 0.00000000 0.00000000 -30.30 0.00 0.00

0.00000000 -0.00020597 0.00000000 0.00 -30.30 0.00

0.00000000 0.00000000 -0.00020597 0.00 0.00 -30.30

Writing output data file pwscf.save

PWSCF : 0.28s CPU time, 0.39s wall time

init_run : 0.05s CPU

electrons : 0.11s CPU

stress : 0.00s CPU

Called by init_run:

wfcinit : 0.01s CPU

potinit : 0.00s CPU

Called by electrons:

c_bands : 0.09s CPU ( 6 calls, 0.015 s avg)

sum_band : 0.01s CPU ( 6 calls, 0.001 s avg)

v_of_rho : 0.00s CPU ( 6 calls, 0.001 s avg)

mix_rho : 0.00s CPU ( 6 calls, 0.000 s avg)

Called by c_bands:

init_us_2 : 0.00s CPU ( 28 calls, 0.000 s avg)

cegterg : 0.09s CPU ( 12 calls, 0.007 s avg)

Called by *egterg:

h_psi : 0.01s CPU ( 35 calls, 0.000 s avg)

g_psi : 0.00s CPU ( 21 calls, 0.000 s avg)

cdiaghg : 0.06s CPU ( 31 calls, 0.002 s avg)

Called by h_psi:

add_vuspsi : 0.00s CPU ( 35 calls, 0.000 s avg)

General routines

calbec : 0.00s CPU ( 37 calls, 0.000 s avg)

cft3s : 0.02s CPU ( 354 calls, 0.000 s avg)

davcio : 0.00s CPU ( 40 calls, 0.000 s avg)

Parallel routines

fft_scatter : 0.01s CPU ( 354 calls, 0.000 s avg)

Mehdi Bozzo-Rey

Open Source Solution Developer

Platform OCS5

Platform computing

Phone: +1 905 948 4649

From: users-bounces@open-mpi.org [mailto:users-bounces@open-mpi.org] On Behalf Of C.Y. Lee
Sent: August-15-08 1:03 PM
To: users@open-mpi.org
Subject: [OMPI users] Segmentation fault (11) Address not mapped (1)

All,

I had a similar problem as James described in an earlier message: http://www.open-mpi.org/community/lists/users/2008/07/6204.php

While he was able to recompile openmpi to solve the problem, I had no luck with my RedHat Enterprise 5 system.

Here are two other threads with similar issues regarding openmpi on Ubuntu and OSX which were solved: https://bugs.launchpad.net/ubuntu/+source/binutils/+bug/234837

http://www.somewhereville.com/?cat=55

Now...

Here is my story:

I had Quantum Espresso (QE) running without problem using openmpi.

However, when I tried to recompile QE with a recompiled fftw-2.1.5, it compiled without any error. But when I ran QE, it gave me the error below:

*** Process received signal ***
Signal: Segmentation fault (11)

Signal code: Address not mapped (1)
Failing at address: 0x22071b70
[ 0] /lib64/libpthread.so.0 [0x352420de70]
[ 1] /usr/lib64/liblapack.so.3(dsytf2_+0xc43) [0x2aaaaac9f5e3]
[ 2] /usr/lib64/liblapack.so.3(dsytrf_+0x407) [0x2aaaaaca0567]
[ 3] /opt/espresso-4.0.1/bin/pw.x(mix_rho_+0x828) [0x5044b8]
[ 4] /opt/espresso-4.0.1/bin/pw.x(electrons_+0xb37) [0x4eae47]
[ 5] /opt/espresso-4.0.1/bin/pw.x(MAIN__+0xbf) [0x42b3af]
[ 6] /opt/espresso-4.0.1/bin/pw.x(main+0xe) [0x6aad5e]
[ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x352361d8a4]
[ 8] /opt/espresso-4.0.1/bin/pw.x [0x42b239]
*** End of error message ***

From what I read from the above links, it seems to be a bug in openmpi.

Please share your thoughts on this, thank you!