General information about NWChem¶
Where is the User’s Manual?¶
The NWChem User’s Manual is now at https://nwchemgit.github.io/Home.html
Where do I go for help with a Global Arrays problem?¶
If you have problems with compiling the tools directory, please visit the Global Arrays Google group at http://groups.google.com/g/hpctools/ or visit the Global Arrays website at http://hpc.pnl.gov/globalarrays/
Where do I go for help with NWChem problems?¶
Please post your NWChem issue to the NWChem forum hosted on Google Groups at https://groups.google.com/g/nwchem-forum
Where do I find the installation instructions?¶
For updated instructions for compiling NWChem please visit the following URL https://nwchemgit.github.io/Compiling-NWChem.html
Installation Problem for the tools directory¶
When compiling the tools directory, you might see the compilation stopping with the message
configure: error: could not compile simple C MPI program
This is most likely due to incorrect settings for the
MPI_LIB, MPI_INCLUDE and LIBMPI environment variables. The
suggested course of action is to unset all of the
three variables above and point your PATH env. variable to the
location of mpif90. If bash is your shell choice, this can be
accomplished by typing
unset MPI_LIB
unset MPI_INCLUDE
unset LIBMPI
export PATH="directory where mpif90 is located":$PATH
What are ARMCI and ARMCI_NETWORK?¶
ARMCI is a library used by Global Arrays (both ARMCI and GA source code
is located in NWChem’s tools directory). More information can be found
at the following URL http://hpc.pnl.gov/armci
If your installation
uses a fast network and you are aiming to get optimal communication
performance, you might want to assign a non-default value to
ARMCI_NETWORK.
The following links contained useful information about
ARMCI_NETWORK:
Input Problem: no output¶
You might encounter the following error message:
! warning: processed input with no task
Have you used emacs to create your input file? Emacs usually does not put and an end-of-line as a last character of the file, therefore the NWChem input parser ignores the last line of your input (the one containing the task directive). To fix the problem, add one more blank line after the task line and your task directive will be executed.
Input problem: AUTOZ fails to generate valid internal coordinates¶
If AUTOZ fails, NWChem will default to using Cartesian coordinates (and ignore any zcoord data) so you don’t have to do anything unless you really need to use internal coordinates. An exception are certain cases where we have a molecule that contains a linear chain of 4 or more atoms, in which case the code will fail (see item 2. for work arounds). For small systems you can easily construct a Z-matrix, but for larger systems this can be quite hard.
First check your input. Are you using the correct units? The default is Angstroms. If you input atomic units but did not tell NWChem, then it’s no wonder things are breaking. Also, is the geometry physically sensible? If atoms are too close to each other you’ll get many unphysical bonds, whereas if they are too far apart AUTOZ will not be able to figure out how to connect things.
Once the obvious has been checked, there are several possible modes of failure, some of which may be worked around in the input.
-
Strictly linear molecules with 3 or more atoms. AUTOZ does not generate linear bend coordinates, but, just as in a real Z-matrix, you can specify a dummy center that is not co-linear. There are two relevant tips:
-
constrain the dummy center to be not co-linear otherwise the center could become co-linear. Also, the inevitable small forces on the dummy center can confuse the optimizer.
- put the dummy center far enough away so that only one connection is generated.
E.g., this input for acetylene will not use internals
geometry
h 0 0 0
c 0 0 1
c 0 0 2.2
h 0 0 3.2
end
but this one will
geometry
zcoord
bond 2 3 3.0 cx constant
angle 1 2 3 90.0 hcx constant
end
h 0 0 0
c 0 0 1
x 3 0 1
c 0 0 2.2
h 0 0 3.2
end
-
Larger molecules that contain a strictly linear chain of four or more atoms (that ends in a free atom). For these molecules the autoz will fail and the code can currently not recover by using cartesians. One has to explicitly define noautoz in the geometry input to make it work. If internal coordinates are required one can fix it in the same manner as described above. However, you can also force a connection to a real nearby atom.
-
Very highly connected systems generate too many internal coordinates which can make optimization in redundant internals less efficient than in Cartesians. For systems such as clusters of atoms or small molecules, try using a smaller value of the scaling factor for covalent radii
zcoord; cvr_scaling 0.9; end
In addition to this you can also try specifying a minimal set of bonds to connect the fragments.
If these together don’t work, then you’re out of luck. Use Cartesians or construct a Z-matrix.
How do I restart a geometry optimization?¶
If you have saved the restart information that is kept in the permanent directory, then you can restart a calculation, as long as it did not crash while writing to the data base.
Following are two input files. The first starts a geometry optimization for ammonia. If this stops for nearly any reason such as it was interrupted, ran out of time or disk space, or exceeded the maximum number of iterations, then it may be restarted with the second job.
The key points are
- The first job contains a START directive with a name for the calculation.
- All subsequent jobs should contain a RESTART directive with the same name for the calculation.
- All jobs must specify the same permanent directory. The default permanent directory is the current directory.
- If you want to change anything in the restart job, just put the data before the task directive. Otherwise, all options will be the same as in the original job.
Job 1.
start ammonia
permanent_dir /u/myfiles
geometry
zmatrix
n
h 1 nh
h 1 nh 2 hnh
h 1 nh 2 hnh 3 hnh -1
variables
nh 1.
hnh 115.
end
end
basis
n library 3-21g; h library 3-21g
end
task scf optimize
Job 2.
restart ammonia
permanent_dir /u/myfiles
task scf optimize
Execution Problem: How do I set the value of ARMCI_DEFAULT_SHMMAX?¶
Some ARMCI_NETWORK values (e.g. OPENIB) depend on the
ARMCI_DEFAULT_SHMMAX value for large allocations of Global memory. We
recommend a value of – at least – 2048, e.g. in bash shell parlance
export ARMCI_DEFAULT_SHMMAX=2048
A value of 2048 for ARMCI_DEFAULT_SHMMAX corresponds to 2048 GBytes,
equal to 204810241024=2147483648 bytes. For
ARMCI_DEFAULT_SHMMAX=2048 to work, it is necessary that kernel
parameter kernel.shmmax to be greater than 2147483648. You can check
the current value of kernel.shmmax on your system by typing
sysctl kernel.shmmax
More detail about kernel.shmmax can be found at this link
WSL execution problems¶
NWChem runs on Windows Subsystem for Linux (WSL) can crash with the error message
--------------------------------------------------------------------------
WARNING: Linux kernel CMA support was requested via the
btl_vader_single_copy_mechanism MCA variable, but CMA support is
not available due to restrictive ptrace settings.
The vader shared memory BTL will fall back on another single-copy
mechanism if one is available. This may result in lower performance.
Local host: hostabc
--------------------------------------------------------------------------
[hostabc:16805] 1 more process has sent help message help-btl-vader.txt / cma-permission-denied
[hostabc:16805] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
The error can be fixed with the following command
echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope
More details at
- https://github.com/Microsoft/WSL/issues/3397#issuecomment-417876710
- https://nwchemgit.github.io/Special_AWCforum/st/id2939/mpirun_nwchem_on_Windows_Subsyst....html
How do I increase the number of digits of the S matrix printout¶
The only way to increase the number of digits of the AO overlap matrix printout is by modify the source code of
the ga_print() function.
For example, in the cagse NWChem 7.0.2, you can do this by editing the C source code in $NWCHEM_TOP/src/tools/ga-5.7.2/global/src/global.util.c by increaseing the number of digits from 5 to 7
--- global.util.c.org 1969-07-20 15:50:45.000000000 -0700
+++ global.util.c 1969-07-20 15:51:19.000000000 -0700
@@ -122,22 +122,22 @@
case C_DBL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj++)
- fprintf(file," %11.5f",dbuf[jj]);
+ fprintf(file," %11.7f",dbuf[jj]);
break;
case C_DCPL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj+=2)
- fprintf(file," %11.5f,%11.5f",dbuf[jj], dbuf[jj+1]);
+ fprintf(file," %11.7f,%11.7f",dbuf[jj], dbuf[jj+1]);
break;
case C_SCPL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj+=2)
- fprintf(file," %11.5f,%11.5f",dbuf[jj], dbuf[jj+1]);
+ fprintf(file," %11.7f,%11.7f",dbuf[jj], dbuf[jj+1]);
break;
case C_FLOAT:
pnga_get(g_a, lo, hi, fbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj++)
- fprintf(file," %11.5f",fbuf[jj]);
+ fprintf(file," %11.7f",fbuf[jj]);
break;
case C_LONG:
pnga_get(g_a, lo, hi, lbuf, &ld);
@@ -229,22 +229,22 @@
case C_DBL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj++)
- fprintf(file," %11.5f",dbuf[jj]);
+ fprintf(file," %11.7f",dbuf[jj]);
break;
case C_FLOAT:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj++)
- fprintf(file," %11.5f",fbuf[jj]);
+ fprintf(file," %11.7f",fbuf[jj]);
break;
case C_DCPL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj+=2)
- fprintf(file," %11.5f,%11.5f",dbuf[jj], dbuf[jj+1]);
+ fprintf(file," %11.7f,%11.7f",dbuf[jj], dbuf[jj+1]);
break;
case C_SCPL:
pnga_get(g_a, lo, hi, dbuf, &ld);
for(jj=0; jj<(jmax-j+1); jj+=2)
- fprintf(file," %11.5f,%11.5f",dbuf[jj], dbuf[jj+1]);
+ fprintf(file," %11.7f,%11.7f",dbuf[jj], dbuf[jj+1]);
break;
default: pnga_error("ga_print: wrong type",0);
}
@@ -761,28 +761,28 @@
if(ndim > 1)
for(j=0; j<(hip[1]-lop[1]+1); j++)
if((double)dbuf_2d[j*bufsize+i]<100000.0)
- fprintf(file," %11.5f",
+ fprintf(file," %11.7f",
dbuf_2d[j*bufsize+i]);
else
fprintf(file," %.5e",
dbuf_2d[j*bufsize+i]);
else
if((double)dbuf_2d[i]<100000.0)
- fprintf(file," %11.5f",dbuf_2d[i]);
+ fprintf(file," %11.7f",dbuf_2d[i]);
else
fprintf(file," %.5e",dbuf_2d[i]);
break;
case C_FLOAT:
if(ndim > 1)
for(j=0; j<(hip[1]-lop[1]+1); j++)
- fprintf(file," %11.5f", fbuf_2d[j*bufsize+i]);
- else fprintf(file," %11.5f", fbuf_2d[i]);
+ fprintf(file," %11.7f", fbuf_2d[j*bufsize+i]);
+ else fprintf(file," %11.7f", fbuf_2d[i]);
break;
case C_DCPL:
if(ndim > 1)
for(j=0; j<(hip[1]-lop[1]+1); j++)
if(((double)dcbuf_2d[(j*bufsize+i)*2]<100000.0)&&((double)dcbuf_2d[(j*bufsize+i)*2+1]<100000.0))
- fprintf(file," %11.5f,%11.5f",
+ fprintf(file," %11.7f,%11.7f",
dcbuf_2d[(j*bufsize+i)*2],
dcbuf_2d[(j*bufsize+i)*2+1]);
else
@@ -792,7 +792,7 @@
else
if(((double)dcbuf_2d[i*2]<100000.0) &&
((double)dcbuf_2d[i*2+1]<100000.0))
- fprintf(file," %11.5f,%11.5f",
+ fprintf(file," %11.7f,%11.7f",
dcbuf_2d[i*2], dcbuf_2d[i*2+1]);
else
fprintf(file," %.5e,%.5e",
@@ -802,7 +802,7 @@
if(ndim > 1)
for(j=0; j<(hip[1]-lop[1]+1); j++)
if(((float)fcbuf_2d[(j*bufsize+i)*2]<100000.0)&&((float)fcbuf_2d[(j*bufsize+i)*2+1]<100000.0))
- fprintf(file," %11.5f,%11.5f",
+ fprintf(file," %11.7f,%11.7f",
fcbuf_2d[(j*bufsize+i)*2],
fcbuf_2d[(j*bufsize+i)*2+1]);
else
@@ -812,7 +812,7 @@
else
if(((float)fcbuf_2d[i*2]<100000.0) &&
((float)fcbuf_2d[i*2+1]<100000.0))
- fprintf(file," %11.5f,%11.5f",
+ fprintf(file," %11.7f,%11.7f",
fcbuf_2d[i*2], fcbuf_2d[i*2+1]);
else
fprintf(file," %.5e,%.5e",
https://nwchemgit.github.io/Special_AWCforum/sp/id3358.html
Linear Dependencies¶
Two or more basis functions can be consider linearly dependent when they span the same region of space. This can result in SCF converge problems. Analysis of the eigenvectors of the S-1/2 matrix (where S is the overlap matrix) is used to detect linear dependencies: if there are eigenvalues close to zero, the basis set goes through the process of canonical orthogonalization (as described in Section 3.4.5 of Szabo & Ostlund “Modern Quantum Chemistry” book). This has net effect of a reduction of number of basis function used, compared to the original number set by input. By setting
set lindep:n_dep 0
this orthogonalization process is skipped.
Discrepancy on the number of basis functions: spherical vs cartesian functions¶
If you are comparing NWChem results with the ones obtained from other codes and you believe there is a
discrepancy in the number of basis functions, keep in mind that NWChem uses cartesian functions by default, while other codes could be using spherical functions, instead.
If you need to use spherical functions, the beginning of the basis input field needs to be
basis spherical
More details in the documentation at the link https://nwchemgit.github.io/Basis.html#spherical-or-cartesian.
See also the following forum entries.
Starting NWChem with mpirun -np 1 crashes¶
This is most likely due to the fact that NWChem was compiled with the setting ARMCI_NETWORK=MPI-PR.
This is the expected behavior, since ARMCI_NETWORK=MPI-PR requires asking for for n+1 processes. In other words, a serial run (with a single computing process) is triggered by executing mpirun -np 2.
If you would prefer mpirun -np 1 to work, other choice of ARMCI_NETWORK are possible as described in the ARMCI documentation.
nb_wait_for_handle Error¶
If you get the following error
{1} nb_wait_for_handle Error: all user-level nonblocking handles have been exhausted
application called MPI_Abort(comm=0x84000002, -1)
you can fix it by executing the following command
export COMEX_MAX_NB_OUTSTANDING=16
Memory errors¶
If you get the following error
[0] Received an Error in Communication: (-1) 0: ptsalloc: increase memory in input line:
you can fix it by either
increasing the memory line in the input file using the syntax described in the Memory section (e.g. memory total 1000 mb), or by
recompiling the NWChem binary with the getmem.nwchem script as described in the section avaible at this
link