Error in .local(.Object, ...) : No such device about bgdata HOT 6 CLOSED

Hi Kayhan,

I am not sure what to make out of "No such device" in this context. Is the .bed file in an unusual location (different file system, different host, ...)? What operating system are you running, and what is your version of R and Rcpp (packageVersion("Rcpp"))?

Thanks,
Alex

from bgdata.

Hi Alex,

The version of R is 3.4.1 . The version of Rcpp is:

> packageVersion("Rcpp")
[1] ‘0.12.14’

and yes the files are in usual places:

-rw-r--r-- 1 batmangh mc560kp      76630 Aug  9 23:47 CG10kAaHg19Clean_v2_Mar2013.fam
-rw-r--r-- 1 batmangh mc560kp   19731078 Aug  9 23:47 CG10kAaHg19Clean_v2_Mar2013.bim
-rw-r--r-- 1 batmangh mc560kp  564562353 Aug  9 23:47 CG10kAaHg19Clean_v2_Mar2013.bed

> m = BEDMatrix('CG10kNhwHg19Clean_v2_Mar2013.bed')
Extracting number of samples and rownames from FAM file...
Extracting number of variants and colnames from BIM file...
Error in .local(.Object, ...) : No such device

the operating system:

[batmangh@br005 Genetics]$ uname -a
Linux br005.pvt.bridges.psc.edu 3.10.0-514.26.2.el7.x86_64 #1 SMP Tue Jul 4 15:04:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

from bgdata.

Hi Kayhan,

thanks, I don't see anything unusual... Maybe your file system does not support memory mapping? Please check the Type column of the df -T CG10kAaHg19Clean_v2_Mar2013.bed output.

Thanks,
Alex

from bgdata.

Thanks Alex,

This is the output:

batmangh@br005 Genetics]$ df -T CG10kAaHg19Clean_v2_Mar2013.bed
Filesystem     Type     1K-blocks          Used    Available Use% Mounted on
/pghbio        fuse 2418185650176 1926487998336 491697651840  80% /pghbio

I don't know that it supports memory mapping or not. Please let me know.

Best,
Kayhan

from bgdata.

@agrueneberg yep, that was the file system issue. I moved the data to a different file system and it worked:

[batmangh@br005 ~]$ df -T CG10kAaHg19Clean_v2_Mar2013.bed
Filesystem                          Type  1K-blocks       Used  Available Use% Mounted on
br001.opa.bridges.psc.edu:/nfs/home nfs4 6440364032 4195274752 2245089280  66% /home

What file systems are compatible with the code? Obviously nfs4 is.

Thanks,
Kayhan

from bgdata.

Hi Kayhan,

what file systems are compatible is an excellent question. My impression was all of them, because I wasn't aware of this issue. You're probably running ZFS behind FUSE, and ZFS should work because we're using that too in combination with NFS. So I guess it has something to do with FUSE? Unfortunately, I don't know enough about those file systems and your system configuration to find an answer to this question, but maybe your sysadmins can give some guidance? All we're doing is basically mmap().

Cheers,
Alex

from bgdata.