[gmx-users] Re: Gromacs 4.6 Installation under Cygwin

[toma0052 at umn.edu]

Hello,
     Thanks for the help. After setting the library path properly, I seem 
to be able to get gromacs up and running. However, I have run into another 
problem with mdrun and actually running any jobs. When I execute
mdrun -v -deffnm Clp_Test -nt 

The output is: Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 8 MPI threads

Followed by several occurrences of:
Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

Then:
starting mdrun 'Martini system for ClpX'
10000 steps,    200.0 ps.

After this however, the simulation never actually begins. I can get rid of 
the error messages by using -pin off, but that doesn't seem to actually fix 
anything. Is there something that has not been installed properly? Below is 
the seemingly relevant portions of the log file generated by the above 
mdrun command.


Log file opened on Mon Feb 25 11:21:08 2013
Host: Theory-Monster  pid: 3192  nodeid: 0  nnodes:  1
Gromacs version:    VERSION 4.6
Precision:          single
Memory model:       32 bit
MPI library:        thread_mpi
OpenMP support:     enabled
GPU support:        disabled
invsqrt routine:    gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:        fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:       enabled
Built on:           Mon, Feb 25, 2013 10:38:04 AM
Built by:           Mike at Theory-Monster [CMAKE]
Build OS/arch:      CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686
Build CPU vendor:   GenuineIntel
Build CPU brand:    Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
C compiler:         /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers 
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer 
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 0.988 nm, Bond, atoms 997 1005
  multi-body bonded interactions: 1.042 nm, G96Angle, atoms 1938 1942
Minimum cell size due to bonded interactions: 1.146 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 1.433 nm
The maximum allowed number of cells is: X 11 Y 11 Z 9
Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Using 8 MPI threads

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Family:  6  Model: 45  Stepping:  7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc 
pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 
tdt x2apic
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256

Table routines are used for coulomb: TRUE
Table routines are used for vdw:     TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.4   Coulomb: 1.2   LJ: 1.2
System total charge: 0.000
Generated table with 1200 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12Shift.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000 r^-6 0.000
Removing pbc first time

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

Initializing Parallel LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------

The number of constraints is 840
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
414 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 4 for couplings
between constraints inside triangles

Linking all bonded interactions to atoms

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 4.02 nm Y 8.04 nm

The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.400 nm
(the following are initial values, they could change due to box deformation)
            two-body bonded interactions  (-rdd)   1.400 nm
          multi-body bonded interactions  (-rdd)   1.400 nm
  atoms separated by up to 5 constraints  (-rcon)  4.021 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 1.400 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.35 Y 0.17
The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.400 nm
            two-body bonded interactions  (-rdd)   1.400 nm
          multi-body bonded interactions  (-rdd)   1.400 nm
  atoms separated by up to 5 constraints  (-rcon)  1.400 nm


Making 2D domain decomposition grid 4 x 2 x 1, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------







> Hello, 
>      I am trying to install Gromacs 4.6 on a Windows workstation under 
> cygwin. After I install everything, when executing g_luck I come up with 
> the error: 
> 'error while loading shared libraries: cyggmx-6.dll: cannot open shared 
> object file: No such file or directory' 
>      There does exist the file cyggmx-6.dll in /usr/local/gromacs/lib 
> and I have tried: export LD_LIBRARY_PATH=/usr/local/gromacs/lib as well 
> as using the flag -BUILD_SHARED_LIBS=OFF with cmake, but neither seem to 
> help. What could be the cause of this?
... [show rest of quote]

For cygwin, you need to have the .dll directory path, 
which  is located at the position given by: 

   -DCMAKE_INSTALL_PREFIX=/my/install/path  trailed by /lib 

in your PATH variable: 

   PATH=/my/install/path/lib:$PATH   mdrun 

(or set it permanent somewhere) 


BTW: with the current cygwin (1.7.17-1), Gromacs 4.6 *does* 
indeed compile fine: 

cmake  -DCMAKE_INSTALL_PREFIX=/usr/local -DGMX_GPU=OFF 
-DGMX_BUILD_OWN_FFTW=OFF  ../gromacs-4.6 

and, more interestingly, runs multithreaded at similar 
performance as compiled with visual studio (tested on Win8/x64).