search

orbeckst / gridcount

DEPRECATED and UNSUPPORTED. gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles").
http://sbcb.bioch.ox.ac.uk/oliver/software/#gridcount
Other
3 stars 0 forks source link

g_ri3Dc fails with 'XDR write failed' #6

Open jsvdvis opened 7 years ago

jsvdvis commented 7 years ago

Dear all,

Whenever I try to use g_ri3Dc in GROMACS version 4.5.7 with options:

g_ri3Dc -f hyper_MD.trr -s hyper_MD.tpr -n hyper.ndx -R 13.5 -z1 -15 -z2 15 -b 1000 -e 150000

I get the following error:

Writing 3D density grid with header {T}149100ps{grp}CHAIN{z1}-15.00{z2}15.00{Rmax}13.50{}0.050{}6655.11{XTC}hyper_MD.trr{Delta}(0.050,0.050,0.050){sumP}9.92277e+08ps

grid_write(): XDR write failed. Writing the 3D grid failed.

An output file is being created, it contains the header line and some unreadable characters. I have also tried several other options with no discernible improvements. It seems something is wrong with XDR, but I have no idea what could be the issue. Could you help me?

Thank you in advance, Jaap

orbeckst commented 7 years ago

Is it always failing or only for one particular example, e.g., did you try a different trajectory, a different selection, different start/end time...

Does your disk have sufficient free space?

Just from seeing the error message I have no idea why XDR write is failing.

orbeckst commented 7 years ago

(Also, because I don't really have the time to support and hack on this tool, I tend to recommend using other tools such as our MDAnalysis Python library https://github.com/orbeckst/gridcount/issues/4#issuecomment-234800589.)

jsvdvis commented 7 years ago

It seems to always fail, I've checked it for several trajectories, index groups and start/end times, as you suggested. I'm also quite sure my system has enough free space (1TB+). Unfortunately, I do not know Python well enough to do anything useful with it for now. I'm planning on studying it in about two months, when I'm supposed to have more free time. For now I will work with g_densmap for the density-calculation.

Thank you for your time!

orbeckst commented 7 years ago

@jsvdvis thanks for trying out different things. From what you are saying it appears indeed to be a more fundamental problem.

Did it ever work for you?

jsvdvis commented 7 years ago

No, it didn't. It seems to me that the calculating (counting) process is working just fine, but the writing process seems to fail.

I'm using a newly installed (about a month ago) version of Xubuntu, if that helps with anything.

Op 21 mei 2017 11:04 schreef "Oliver Beckstein" notifications@github.com:

@jsvdvis https://github.com/jsvdvis thanks for trying out different things. From what you are saying it appears indeed to be a more fundamental problem.

Did it ever work for you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/orbeckst/gridcount/issues/6#issuecomment-302924423, or mute the thread https://github.com/notifications/unsubscribe-auth/AbWQtCmAWOJVn-uAFnGrPhsiVbZT8_J-ks5r7_4FgaJpZM4NaJFq .

orbeckst commented 7 years ago

I haven't compiled gridcount in a while. Maybe something subtle changed in the xdr libraries (although unlikely).

Did you see any "obvious" warnings when you compiled?

-- Oliver Beckstein email: orbeckst@gmail.com

Am May 21, 2017 um 02:10 schrieb jsvdvis notifications@github.com:

No, it didn't. It seems to me that the calculating (counting) process is working just fine, but the writing process seems to fail.

I'm using a newly installed (about a month ago) version of Xubuntu, if that helps with anything.

Op 21 mei 2017 11:04 schreef "Oliver Beckstein" notifications@github.com:

@jsvdvis https://github.com/jsvdvis thanks for trying out different things. From what you are saying it appears indeed to be a more fundamental problem.

Did it ever work for you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/orbeckst/gridcount/issues/6#issuecomment-302924423, or mute the thread https://github.com/notifications/unsubscribe-auth/AbWQtCmAWOJVn-uAFnGrPhsiVbZT8_J-ks5r7_4FgaJpZM4NaJFq .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

jsvdvis commented 7 years ago

The only thing I can remember was some error with the libraries (not the ones you have to give the path to in the Makefile, I can't remember the exact name), which was solved when I added them to the library path.

2017-05-22 18:04 GMT+02:00 Oliver Beckstein notifications@github.com:

I haven't compiled gridcount in a while. Maybe something subtle changed in the xdr libraries (although unlikely).

Did you see any "obvious" warnings when you compiled?

-- Oliver Beckstein email: orbeckst@gmail.com

Am May 21, 2017 um 02:10 schrieb jsvdvis notifications@github.com:

No, it didn't. It seems to me that the calculating (counting) process is working just fine, but the writing process seems to fail.

I'm using a newly installed (about a month ago) version of Xubuntu, if that helps with anything.

Op 21 mei 2017 11:04 schreef "Oliver Beckstein" < notifications@github.com>:

@jsvdvis https://github.com/jsvdvis thanks for trying out different things. From what you are saying it appears indeed to be a more fundamental problem.

Did it ever work for you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/orbeckst/gridcount/issues/6#issuecomment-302924423 , or mute the thread https://github.com/notifications/unsubscribe-auth/AbWQtCmAWOJVn- uAFnGrPhsiVbZT8_J-ks5r7_4FgaJpZM4NaJFq .

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/orbeckst/gridcount/issues/6#issuecomment-303144566, or mute the thread https://github.com/notifications/unsubscribe-auth/AbWQtMSt5_emRifZCM4z2VHdwdmDpgSGks5r8bH9gaJpZM4NaJFq .