dccm calc for large protein hangs on Mac OSX R-console

[visvaldask]

On Mac OSX (High Sierra) when I run cm <- dccm(modes) on a console, the computer becomes very slow and eventually I have to kill the R-console. The protein has two chains, 956 aa residues total. Same story with m.aa <- aanma(pdb, outmodes="calpha") with all atoms, I think the program stalls at the "extracting effective Hessian matrix" step.

I tried to run the first command (dccm) on my Linux desktop in a terminal R session, and it showed a nice progress bar (it would be cool to get one on mac R-console!), and it was able to finish dssm calculation in about one or two minutes. Actually my Linux box is not very fancy, it has 3.2 GB memory vs Macbook's 4 GB, and the former has two processors and the latter 4.

The next thing I can think of is to run R in a terminal on Mac, but I haven't tried that yet... should I?

[visvaldask]

Update: starting R in a terminal was easier than I thought:) and I do see a progress bar in the terminal. Unfortunately, the dccm program seems stalls at 1%...

[visvaldask]

Ok, it's me again... On terminal the job finished in about half hour, and I have to thank progress bar in the terminal for being able to follow it though:) I guess it's a non-issue then (although I do wish the progress bar was on R-console, the editing there is kinda neat)...

[Barry Grant]

Thanks for posting this - it is good to know we might have issues here.

Can I ask: Do you mean the "R-console" in RStudio? Or some other place?

On your Mac it should not take that long. So we should looking this further. Perhaps you have an older version of the bio3d package or R itself - you can check with the sessionInfo() function on both your machines and let us know please.

Alternatively there could be something else on your laptop eating up RAM hence slowing down your calculation. Perhaps try a restart when you get the opportunity.

[visvaldask]

I shut down my mac so many times yesterday, but the program doesn't seem to run faster or stop freezing the computer. I guess it is paging excessively... I think I will do these calculations on Linux; actually for my MD trajectory dccm analysis even on Linux I had to reduce all pdb to Calphas, because R complained about not being handle 4.2 GB vectors (which is beyond the total memory).

Ok, on Mac R package was taken from here: https://cran.r-project.org/bin/macosx/. "R console" shows up as the title of the GUI which appears when I invoke R through Applications menu. "Terminal" version of R appears when I invoke R through the command line in a terminal. Now, sessionInfo: Ubuntu Linux:

sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=lt_LT.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=lt_LT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=lt_LT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=lt_LT.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] bio3d_2.3-3

loaded via a namespace (and not attached): [1] magrittr_1.5 parallel_3.2.3 igraph_1.1.2 Rcpp_0.12.14
[5] grid_3.2.3 pkgconfig_2.0.1

MacOS:

sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.2

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] bio3d_2.3-3

loaded via a namespace (and not attached): [1] compiler_3.4.3 parallel_3.4.3 Rcpp_0.12.14 grid_3.4.3

I will also use this opportunity to note that on some occasions I have to specify pymol as exefile="/sw/bin/pymol" (it's in the search PATH!) when bio3d has to launch pymol, because the program keeps looking for MacPymol in Applications (which I don't have). I haven't found a configuration file where I could change this behavior.

[visvaldask]

If it's of any (further) help, even in tutorial exercise "Protein Structure Networks with Bio3D" command "cij<-dccm(modes)" near the beginning of the tutorial takes incredibly long time (or perhaps it just hangs) on Mac R console while on both Mac Terminal and on Linux it takes just couple of seconds!

[visvaldask]

I don't want to open another ticket, but just to say: using "view" function does not work on neither Mac or Linux:

view.cna(net, pdb, launch = TRUE) Error: could not find function "view.cna" If I replace ""view" with "vmd" in the command above it does work.

[visvaldask]

If I try "Network generation from molecular dynamics data" example, I get this both on Linux and MacOs terminals:

view.dccm(cij, pdb, launch = TRUE) Error: could not find function "view.dccm" vmd.dccm(cij, pdb, launch = TRUE) Error: could not find function "vmd.dccm" view.cna(net, pdb) Error: could not find function "view.cna" vmd.cna(net, pdb)

However, with vmd.cn nothing happens (no vmd frame appears), it just goes to next prompt without action.

[visvaldask]

interestingly, "vmd.cna(net, pdb, launch = TRUE)" from the example higher up ("Network generation from normal mode analysis data") does invoke vmd, so there is something wrong with the "view" aka "vmd" command.

Sorry for so many messages.

[Xinqiu Yao]

Hi,

Yes, the name has changed from 'view.XXX' to 'vmd.XXX' or 'pymol.XXX' in several functions. We will update tutorials shortly.

[visvaldask]

Thank you Xin-Qiu Yao! Just please bear in mind that "vmd.cna(net, pdb, launch = TRUE)" command is a bit broken; in the "Network generation from molecular dynamics data" the launch does not take place, I had to invoke vmd manually from the created network.vmd and network.pdb files. According to documentation, the command vmd.cna(args) really should be vmd(args), but I haven't figured it out yet. Thankfully, I have a workaround though.

[Xinqiu Yao]

Thanks for reminding. I will check the 'launch' option.

You can call either 'vmd.cna(x)' or 'vmd(x)' - They should have the same effect as long as 'x' is a 'cna' object.

[Xinqiu Yao]

Update online documents for cna vignette. Check the user proposed vmd.cna(..., launch=TRUE) problem.

[Xinqiu Yao]

Found a VMD launching problem on Windows and have fixed by this commit.

Not sure if this solves your problem also. Let me know if it doesn't, and tell me what OS and command you were exactly using.

[visvaldask]

I will have to figure how to install Bio3d from bitbucket, but I am good for now, and also bit swamped in proposal writing, will try later... Thank you for the fantastic work you are doing!

[Xinqiu Yao]

Resolved by recent commits. Could be reopened if the user returns with additional questions.