VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Mar 21 2019 - 17:34:38 CDT

Found the problem. Here is my input:

!RI BP86 OPT def2-SVP def2/J NOSOSCF CPCM(Water) Grid5 NoFinalGrid EnGrad NormalSCF printbasis
%output PrintLevel Mini Print[ P_Mulliken ] 1 Print[P_AtCharges_M] 1 end
%output Print[ P_Basis ] 2 Print[ P_MOs ] 1 end
 %scf
 maxiter 2000
 shift shift 0.1 erroff 0 end
 damp fac 0.80 erroff 0.0001 end
 end

Notice that I have printbasis in the input line and I have the output command (2nd line) with another print command. I think this was corrupting my output. After deleting printbasis from the input line, I can now open the ORCA output in VMD.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Thursday, March 21, 2019 3:41 PM
To: McGuire, Kelly; vmd-l_at_ks.uiuc.edu
Subject: RE: VMD OrcaPlugin Bug

Oof. This isn't nessicarily a memory leak, but could just be memory being accessed before it is allocated. In any event, the stack trace seems to indicate that the offending code/input is somewhere in the close_orca_read function in the plugins/molfile_plugin/src directory. Its a new plugin, so I suspect that the range of attempted input didn't consider your input format.

-Josh

On 2019-03-21 14:10:50-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

  Sometimes, the console prints this out also:
terminate called after throwing an instance of 'std::bad_alloc'
  what(): std::bad_alloc
Abort
  So, it seems like a memory leak? The ORCA output is only 420 KB...

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Thursday, March 21, 2019 12:49 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: VMD OrcaPlugin Bug
 I ran a QM (NOT QMMM) simulation on a small molecule, but tried to open the ORCA output in VMD 1.9.4a12 because I know this version of VMD can still open orbitals correctly. At least, I can open the ORACA orbitals from my QMMM simulations. But, with this QM simulation I get a segmentation fault and VMD crashes. I ran the debugger and then typed where. This is the result:
(gdb) where
#0 0x00007ffff05bd207 in raise () from /lib64/libc.so.6
#1 0x00007ffff05be8f8 in abort () from /lib64/libc.so.6
#2 0x00007ffff05ffd27 in __libc_message () from /lib64/libc.so.6
#3 0x00007ffff0608489 in _int_free () from /lib64/libc.so.6
#4 0x00007fff8d469cf5 in close_orca_read(void*) ()
   from /panfs/pan.fsl.byu.edu/scr/grp/busathlab/kmcguir2/m2drugsimulations/VMD194/vmd194a12/lib/vmd/plugins/LINUXAMD64/molfile/orcaplugin.so
#5 0x0000000000839caf in MolFilePlugin::~MolFilePlugin() ()
#6 0x000000000078875c in CoorPluginData::next(Molecule*) ()
#7 0x000000000083013a in Molecule::prepare() ()
#8 0x000000000078e6ec in Displayable::draw_prepare() ()
#9 0x000000000078e716 in Displayable::draw_prepare() ()
#10 0x000000000089d395 in Scene::prepare() ()
#11 0x00000000008c8d71 in VMDApp::VMDupdate(int) ()
#12 0x000000000
I don't know what to make of this. I don't have the background to interpret the cause.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602