Re: [Open-ms-general] Error: unable to open primary document entity

[Archie C. <ar...@de...>]

Replying to myself...

On Fri, Jan 6, 2012 at 1:50 PM, Archie Cobbs <ar...@de...> wrote:

> Error: Unable to read file (- due to that error of type Parse Error in:
>
> /usr/src/packages/BUILD/openms-1.9pre9428/source/FORMAT/HANDLERS/XMLHandler.C@89
>     -void
> OpenMS::Internal::XMLHandler::fatalError(OpenMS::Internal::XMLHandler::ActionMode,
>     const OpenMS::String&, OpenMS::UInt, OpenMS::UInt) const)
>
> /usr/src/packages/BUILD/openms-1.9pre9428/source/FORMAT/HANDLERS/XMLHandler.C(88):
>     While loading 'file.mzML': unable to open primary document entity
> '/home/archie/proj/ppt/test/file.mzML'
>
> When I shorten the file to the first 10,000 lines (and terminate the XML),
> the problem goes away.
>
> Not sure what this means. Is 3.5MB too large for OpenMS? Maybe there is a
> 32-bit file length value overflow somewhere?
>

This does appear to be the problem. Running OpenMS on large files using a
32-bit machine doesn't seem to work.

Below is some of the strace(1) output from an invocation of
NoiseFilterGaussian. You can see that several open(2) invocations that are
using O_LARGEFILE succeed, but then there is one that does not and it
fails. This is probably one of the included libraries (xerces?)

...
open("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY|O_LARGEFILE) = 3
read(3, "<?xml version=\"1.0\" encoding=\"is"..., 8191) = 8191
close(3)                                = 0
open("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY|O_LARGEFILE) = 3
read(3, "<?xml version=\"1.0\" encoding=\"is"..., 8191) = 8191
close(3)                                = 0
stat64(".", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
getcwd("/home/archie/proj/ppt/test", 4096) = 27
stat64("/usr/share/OpenMS", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
stat64("/usr/share/OpenMS//CV/psi-ms.obo", {st_mode=S_IFREG|0644,
st_size=415352, ...}) = 0
open("/usr/share/OpenMS/CV/psi-ms.obo", O_RDONLY|O_LARGEFILE) = 3
read(3, "format-version: 1.2\ndate: 22:11:"..., 8191) = 8191
read(3, "em.\" [PSI:MS]\nrelationship: part"..., 8191) = 8191
.... snip ...
read(3, "05 ! quantification datatype\n\n[T"..., 8191) = 8191
read(3, "transition validation attribute\n"..., 8191) = 5802
read(3, "", 8191)                       = 0
brk(0x93b8000)                          = 0x93b8000
close(3)                                = 0
stat64("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
{st_mode=S_IFREG|0444, st_size=3568219846, ...}) = 0
open("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY|O_LARGEFILE) = 3
read(3, "<?xml version=\"1.0\" encoding=\"is"..., 8191) = 8191
getcwd("/home/archie/proj/ppt/test", 4097) = 27
*open("/home/archie/proj/ppt/usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY) = -1 EOVERFLOW (Value too large for defined data type)*
open("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY|O_LARGEFILE) = 4
read(4, "<?xml version=\"1.0\" encoding=\"is"..., 8191) = 8191
close(4)                                = 0
open("../usb-drive-contents/ControlPooled_200ng.wiff.MZML",
O_RDONLY|O_LARGEFILE) = 4
read(4, "<?xml version=\"1.0\" encoding=\"is"..., 8191) = 8191
close(4)                                = 0
close(3)                                = 0
time(NULL)                              = 1325892584
fstat64(1, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 0), ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =
0xb76f7000
write(1, "Error: Unable to read file (- du"..., 299Error: Unable to read
file (- due to that error of type Parse Error in:
/usr/src/packages/BUILD/openms-1.9pre9428/source/FORMAT/HANDLERS/XMLHandler.C@89-voidOpenMS::Internal::XMLHandler::fatalError(OpenMS::Internal::XMLHandler::ActionMode,
const OpenMS::String&, OpenMS::UInt, OpenMS::UInt) const)
) = 299

I guess I will have to find a bigger machine...

-Archie

-- 
Archie L. Cobbs