Internal PLUMED error / file Action.cpp, line 215 / Segmentation fault

[billy.willi...@gmail.com]

Hi Plumed Users and Developers,

We are using Plumed version 2.2.1 and following the Plumed 2.1.5 'Tutorial 1' as linked here:

Belfast Tutorial 1.

We compiled Plumed successfully using Suze v43.1, GCC 4.8.5 on a local machine and imputed the following command:

plumed driver --ixyz trajectory-short.xyz --plumed plumed.dat --length-units 0.1

The trajectory-short.xyz file came from the Belfast Tutorial linked above and contents of plumed.dat were as follows:

#printout frequency
PRINT ARG=cvdist STRIDE=1 FILE=COLVAR
#my first plumed input:
DISTANCE ATOMS=2,253 LABEL=e2edist
#endofinput
ENDPLUMED

When running Plumed, I get the following printed onto the screen:

PLUMED: PLUMED is starting
PLUMED: Version: 2.2.1 (git: Unknown) compiled on Mar 14 2016 at 17:23:39
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed-code.org
PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 256
PLUMED: File suffix:
PLUMED: FILE: plumed.dat
PLUMED: Action PRINT
PLUMED:   with label @0
PLUMED:   with stride 1
PLUMED: ERROR in input to action PRINT with label @0 : cannot find action named cvdist (hint! the actions in this ActionSet are: )
PLUMED: 


********** STACK DUMP **********
plumed(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x3f) [0x6880e7]
plumed(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x30) [0x6884fe]
plumed(_ZNK4PLMD6Action5errorERKSs+0x133) [0x578bd1]
plumed(_ZN4PLMD19ActionWithArguments21interpretArgumentListERKSt6vectorISsSaISsEERS1_IPNS_5ValueESaIS7_EE+0x1ac5) [0x582597]
plumed(_ZN4PLMD19ActionWithArguments17parseArgumentListERKSsRSt6vectorIPNS_5ValueESaIS5_EE+0x4e) [0x583bf4]
plumed(_ZN4PLMD19ActionWithArgumentsC2ERKNS_13ActionOptionsE+0xe5) [0x583f7f]
plumed(_ZN4PLMD7generic5PrintC1ERKNS_13ActionOptionsE+0x5b) [0x5e7925]
plumed(_ZN4PLMD7generic17PrintRegisterMe816createERKNS_13ActionOptionsE+0x29) [0x5e7f9b]
plumed(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x4bd) [0x57c0b7]
plumed(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorISsSaISsEE+0x21b) [0x5a5abb]
plumed(_ZN4PLMD10PlumedMain13readInputFileESs+0x14a) [0x5a5e2c]
plumed(_ZN4PLMD10PlumedMain4initEv+0x337) [0x5a62d7]
plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x28eb) [0x5a8d2f]
plumed(plumedmain_cmd+0xce) [0x5aff14]
plumed(plumed_cmd+0x32) [0x70be1b]
plumed(_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE+0x2043) [0x509863]
plumed(_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE+0x13c3) [0x593d61]
plumed(_ZN4PLMD10CLToolMain3cmdERKSsPv+0x918) [0x59526c]
plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x5a50) [0x5abe94]
plumed(plumedmain_cmd+0xce) [0x5aff14]
plumed(plumed_cmd+0x32) [0x70be1b]
plumed(main+0xdf) [0x4a21fb]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f6b45a81b25]
plumed() [0x4a2039]
******** END STACK DUMP ********

+++ Internal PLUMED error
+++ file Action.cpp, line 215
+++ message: ERROR in input to action PRINT with label @0 : cannot find action named cvdist (hint! the actions in this ActionSet are: )
Segmentation fault

Any help on solving this problem would be appreciated.

Cheers,

Billy

[Omar Valsson]

Hello, 

The problem is that your plumed.dat file doesn’t make sense. You are trying to write out the value of a collective variable (with the label cvdist) that hasn’t been defined. You always need to define the CVs before writing them out using the PRINT action. 

The following input should work instead

DISTANCE ATOMS=2,253 LABEL=e2edist

PRINT ARG=e2dist STRIDE=1 FILE=COLVAR

ENDPLUMED

Here you calculate the CV with the label e2dist that is the distance between atoms 2 and 253 and print out the value at every step.

Regards,

Omar

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[gareth....@gmail.com]

Hello

You need to swap round your input file and have the distance command before the print command.

Gareth

Sent from my iPad

--

[billy.willi...@gmail.com]

Thank you Omar,

I have followed your advice literally and have received this error.  What I did was paste this:

DISTANCE ATOMS=2,253 LABEL=e2edist

PRINT ARG=e2dist STRIDE=1 FILE=COLVAR

ENDPLUMED

Into the plumed.dat file and it returned the same message.

Is there another tutorial available or any other documentation, that doesn't assume prior knowledge of Plumed?  Because it seems that based on what you're saying, if anyone follows the above tutorial to the letter, they are going to get this error.  Is there perhaps another thread where someone has brought this up?

Regards,
Billy

Billy

[Massimiliano Bonomi]

There is a typo

The cv is called 

e2edist

but then you try to print

e2dist

Max

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[billy.willi...@gmail.com]

Hi Gareth,

I followed your advice and changed plumed.dat to this:

DISTANCE ATOMS=2,253 LABEL=e2edist
PRINT ARG=cvdist STRIDE=1 FILE=COLVAR
ENDPLUMED

I received the same error:

PLUMED: PLUMED is starting
PLUMED: Version: 2.3b (git: Unknown) compiled on Aug 16 2016 at 18:01:46

PLUMED: Please cite this paper when using PLUMED [1]

PLUMED: For further information see the PLUMED web page at http://www.plumed.org

PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 256
PLUMED: File suffix:
PLUMED: FILE: plumed.dat

PLUMED: Action DISTANCE
PLUMED:   with label e2edist
PLUMED:   between atoms 2 253
PLUMED:   using periodic boundary conditions
PLUMED: Action PRINT
PLUMED:   with label @1
PLUMED:   with stride 1
PLUMED: ERROR in input to action PRINT with label @1 : cannot find action named cvdist (hint! the actions in this ActionSet are: e2edist )

PLUMED: 


********** STACK DUMP **********

plumed(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x3f) [0x786437]
plumed(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x28) [0x786be8]
plumed(_ZNK4PLMD6Action5errorERKSs+0x148) [0x5cb00e]
plumed(_ZN4PLMD19ActionWithArguments21interpretArgumentListERKSt6vectorISsSaISsEERS1_IPNS_5ValueESaIS7_EE+0x20e0) [0x5d5f26]
plumed(_ZN4PLMD19ActionWithArguments17parseArgumentListERKSsRSt6vectorIPNS_5ValueESaIS5_EE+0x2b4) [0x5d7d7a]
plumed(_ZN4PLMD19ActionWithArgumentsC2ERKNS_13ActionOptionsE+0x1ba) [0x5d8024]
plumed(_ZN4PLMD7generic5PrintC1ERKNS_13ActionOptionsE+0x5b) [0x658f83]
plumed(_ZN4PLMD7generic17PrintRegisterMe816createERKNS_13ActionOptionsE+0x21) [0x659868]
plumed(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x523) [0x5cff4b]
plumed(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorISsSaISsEE+0x33b) [0x5ffba5]
plumed(_ZN4PLMD10PlumedMain13readInputFileESs+0x184) [0x602cda]
plumed(_ZN4PLMD10PlumedMain4initEv+0x385) [0x60320d]
plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x3618) [0x6069d6]
plumed(plumedmain_cmd+0xed) [0x6107e7]
plumed(plumed_cmd+0x23) [0x8219d3]
plumed(_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE+0x2842) [0x521d62]
plumed(_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE+0x1716) [0x5e9c66]
plumed(_ZN4PLMD10CLToolMain3cmdERKSsPv+0xa8b) [0x5eb6e1]
plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x7757) [0x60ab15]
plumed(plumedmain_cmd+0xed) [0x6107e7]
plumed(plumed_cmd+0x23) [0x8219d3]
plumed(main+0x79) [0x4942d6]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fb6ca8a2b25]
plumed() [0x494199]

******** END STACK DUMP ********

+++ Internal PLUMED error

+++ file Action.cpp, line 233
+++ message: ERROR in input to action PRINT with label @1 : cannot find action named cvdist (hint! the actions in this ActionSet are: e2edist )
Abort

Regards,

Billy
~           

[Massimiliano Bonomi]

Hi,

please follow Omar suggestion with the corrected typo of your last email,

and you will get rid of the error.

Max

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/1badf247-5bf9-4e8f-9618-990adef9f1c9%40googlegroups.com.

[billy.willi...@gmail.com]

Thanks Max, it's working now.  :)

Billy

[Massimiliano Bonomi]

;-)

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/5eb12582-0e6e-411d-b0e6-075ee394163b%40googlegroups.com.