Error while trying to run Ensemble All-Atom NMA for more than 8 structures

[Ashraya]

Hi,

I first tried to run ensemble all-atom NMA using aanma.pdbs on 59 structures using the following command:

aln <- pdbaln(pdbs_files) #creating multiple sequence alignment from list of pdb files
pdbs <- read.all(aln) #reading the alignment
modes<-aanma.pdbs(pdbs,subspace = 2)

After running aanma.pdbs, it gave the following error:

Warning in mclapply(1: length(all.pdb), function(i) { : scheduled cores 9, 2 encountered errors in user code, all values of the jobs will be affected

Beyond this, the job just gets killed and I have to restart a new R session. I tested out this with very less number of structures and I did not face any problem till there were 8 structures in the input. Beyond that, the same error starts coming and the job gets killed. I also tried out the same by providing values for nproc parameter in aanma.pdbs, but to no avail.

Following in the output of my sessionInfo():

>sessionInfo()
R version 3.4.1 (2017-06-30)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 16.04.4 LTS
 Matrix products: default
 BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
 LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_IN.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C    

other attached packages:
[1] bio3d_2.3-4

loaded via a namespace (and not attached):
 [1] colorspace_1.3-2 scales_0.4.1     compiler_3.4.1   lazyeval_0.2.0   plyr_1.8.4       parallel_3.4.1   tools_3.4.1      gtable_0.2.0    
 [9] tibble_1.3.0     Rcpp_0.12.10     ggplot2_2.2.1    grid_3.4.1       munsell_0.4.3   

Any help or explanation will be appreciated. Thank you in advance

[Lars Skjærven]

can you try with argument ncore=1 to the aanma() ?

[Lars Skjærven]

Install the latest bugfix for this issue with the following commands:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

that should fix the issue

[Yazhini arangas]

This solution is not working. Basically, if sequence alignment has gaps, this error is persistent. The error is only for aanma.pdbs() and not for nma.pdbs() function. This needs to be fixed asap since ensemble all-atom NMA function is frequently used.

[Lars Skjærven]

Do you still get the same mclapply error when passing argument ncore=1 as proposed above?

[Yazhini arangas]

yes. when I give ncore=1 in aanma.pdb(), it throw the same message 'warning in mclapply(1:length(all.pdb), function(i) { : scheduled core 1 encountered error in user code, all values of the job will be affected'. In aanma() function, aanma(read.all(a1), ncore = 1) gives an error as Error in fit.xyz(pdbs$xyz[1, ], pdb$xyz, gaps.pos$f.inds, nogap.indsi$xyz) : length of 'fixed.inds' != length of 'mobile.inds' with warning message: Warning in if (is.factor(x)) { : closing unused connection 3 (/tmp/RtmpILRLHI/file286510fd6cef)

[Yazhini arangas]

After trying few things, I noticed that if file name contains special characters (like /or ../), then it causes such error. If I put all input PDB files in current directory and run the same command, It runs normally.

Thank you.