[ensembl-dev] "Too many concurrent connections" errors when using get_all_Alleles()
Will McLaren
wm2 at ebi.ac.uk
Tue Jul 12 11:42:51 BST 2016
Glad that seems to be working.
Do keep us posted if you encounter any more problems.
Cheers
Will
On 12 July 2016 at 11:32, <andrew126 at mac.com> wrote:
> Hi Will,
>
> I think I've solved it .. I didn't realize/notice, by default, VirtualBox
> puts VMs on a different network than the host .. putting the VM in bridged
> mode gets it on the same network as the host (and the rest of my network),
> and that seems to have resolved things (so far .. knock on wood). I'm
> surprised so much worked with the VM being on a different network (?), but
> I'm happy things are working at the moment.
>
> Thanks for all the help.
>
> Cheers,
>
> Andrew
>
>
> On Jul 12, 2016, at 5:25 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
> Try this path for the downloads:
>
>
> ftp://ftp.ensembl.org/pub/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/
>
> It works fine for me.
>
> I'll have a look into your VM test, though this sounds like low level
> network stuff that I would have no idea how to debug!
>
> Will
>
> On 12 July 2016 at 02:04, <andrew126 at mac.com> wrote:
>
>> Hi Will,
>>
>> Here's some more that I've done.
>>
>> I was unable to download the VCFs locally based on the link you provided (
>> ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/), since those
>> files are small (~170-byte), I assume they are links to other files, but I
>> couldn't establish the location of the linked-to files.
>>
>> For example, it appears that
>> variation_genotype/homo_sapiens/ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi
>> points to
>> release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi
>> ... but ftp.ensembl.org/pub/release-82 is an empty directory (to my
>> browser).
>>
>> To standardize things as much as possible, I downloaded/installed
>> Ensembl84VirtualMachine.ova. Note that it didn't have IPC-Run installed on
>> it. I installed IPC-Run 0.79, updated the ensembl 84 git, and then ran the
>> test code.
>>
>> On the first run after booting, the test code runs successfully for a
>> short period of time before crashing.
>>
>> Before crashing stderr reports these messages:
>> [get_local_version] downloading the index file...
>> [get_local_version] downloading the index file...
>>
>> which seem to refer to these files getting downloaded:
>>
>> ALL.chr1.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi
>>
>> ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi
>>
>> Given that the slice referenced in the perl script is chr 4, I have no
>> idea why chr 1 is getting downloaded (?) .. do you see the same thing when
>> you run the script?
>>
>> After the crash, netstat shows large number of ensembl connections, most
>> in FIN_WAIT2 state:
>>
>> ...
>> 7fff629ec000-7fff629ee000 r--p 00000000 00:00 0
>> [vvar]
>> 7fff629ee000-7fff629f0000 r-xp 00000000 00:00 0
>> [vdso]
>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> [vsyscall]
>> Aborted (core dumped)
>> ensembl at ensembl:~$ netstat | more
>> Active Internet connections (w/o servers)
>> Proto Recv-Q Send-Q Local Address Foreign Address State
>>
>> tcp 0 0 10.0.2.15:44305 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44321 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:43142 ec2-50-16-247-22.:mysql
>> TIME_WAIT
>> tcp 0 0 10.0.2.15:44303 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44313 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44289 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:35143 ec2-23-21-181-179:mysql
>> TIME_WAIT
>> tcp 0 0 10.0.2.15:44295 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44309 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44319 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44293 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44287 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44323 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44283 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44269 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp 0 0 10.0.2.15:44317 ftp-ensembl-ext.san:ftp
>> FIN_WAIT2
>> tcp6 0 0 localhost:48000 localhost:ipp
>> ESTABLISHED
>> tcp6 0 0 localhost:ipp localhost:48000
>> ESTABLISHED
>> Active UNIX domain sockets (w/o servers)
>> Proto RefCnt Flags Type State I-Node Path
>> unix 18 [ ] DGRAM 10253 /dev/log
>> Etc.
>>
>> From google (I have no idea the level of credibility):
>> "FIN_WAIT2 is a state when the server closes the socket on its side but
>> does not receive an acknowledgement of the close from the client. Does
>> your application open and close a lot of connections? When you close on
>> the client side do you use the Connection.close() method?"
>>
>> Even after the active-internet-connections table clears, I get
>> more-instantaneous crashes. After these, netstat shows:
>>
>> Active Internet connections (w/o servers)
>> Proto Recv-Q Send-Q Local Address Foreign Address State
>>
>> tcp 0 0 10.0.2.15:40289 ec2-50-16-247-22.:mysql
>> TIME_WAIT
>> tcp 0 0 10.0.2.15:59322 ec2-23-21-181-179:mysql
>> TIME_WAIT
>> tcp 0 0 10.0.2.15:59321 ec2-23-21-181-179:mysql
>> TIME_WAIT
>> tcp6 1 0 localhost:55452 localhost:ipp
>> CLOSE_WAIT
>> Active UNIX domain sockets (w/o servers)
>> Proto RefCnt Flags Type State I-Node Path
>> unix 19 [ ] DGRAM 10189 /dev/log
>> unix 3 [ ] STREAM CONNECTED 14690
>> Etc.
>>
>> If I wait an extended period of time (~30 minutes), then the test code
>> will not instantaneously crash and it will behave how it behaved initially:
>> running successfully for a short period of time and then crashing (though
>> not nec. at the exact same spot).
>>
>> Please let me know if these notes offer you any insights, or if you can
>> suggest anything else for me to try .. I'd really like to get this working.
>>
>> Many thanks,
>>
>> Andrew
>>
>>
>>
>>
>>
>>
>>
>>
>> On Jul 11, 2016, at 10:44 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>
>> Hi again,
>>
>> I can't get the script to recreate the issue at my end.
>>
>> I'm surprised you're getting that message as the script is querying only
>> one chromosome, so it should only be opening one (at most two) VCFs
>> concurrently.
>>
>> I don't know what's happening underneath our API layer, but my guess
>> would be some other process (possibly zombie?) has an open connection to
>> our FTP site. It may also be there's some per-IP allowance that is being
>> violated somehow?
>>
>> In any case have you tried downloading the VCFs locally?
>>
>> Cheers
>>
>> Will
>>
>> On 11 July 2016 at 14:52, <andrew126 at mac.com> wrote:
>>
>>> Hi,
>>>
>>> In case it helps to debug this issue, I've reattached the perl script
>>> that throws "too many connection" errors .. even with the release/84 code
>>> fix.
>>>
>>> Many thanks,
>>>
>>> Andrew
>>>
>>> use strict;
>>> $|=1;
>>> use IPC::Run;
>>> use Bio::EnsEMBL::Registry;
>>> use Bio::EnsEMBL::ApiVersion;
>>> printf( "The API version used is %s\n", software_version() );
>>>
>>> my $registry = 'Bio::EnsEMBL::Registry';
>>> $registry->load_all();
>>> $registry->set_reconnect_when_lost();
>>> $registry->load_registry_from_db(
>>> -host => 'useastdb.ensembl.org',
>>> -user => 'anonymous'
>>> );
>>>
>>> my $gene_adaptor = $registry->get_adaptor('homo_sapiens','core','gene');
>>> my $slice_adaptor =
>>> $registry->get_adaptor('homo_sapiens','core','slice');
>>>
>>> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "4",
>>> 139000000, 139100000);
>>>
>>> print "Variation:\n";
>>>
>>> my $vf_adaptor = $registry->get_adaptor( 'human', 'variation',
>>> 'variationfeature' );
>>> $vf_adaptor->db->use_vcf(1);
>>> my $vars = $vf_adaptor->fetch_all_by_Slice($slice);
>>>
>>> foreach my $vf (@{$vars}){
>>> print "\t".$vf->variation_name(),"\n";
>>> print "\t".$vf->allele_string(),"\n";
>>> print "\tChromosome: ".$slice->seq_region_name."\n";
>>> print "\tStart-End:
>>> ".$vf->seq_region_start."-".$vf->seq_region_end."\n";
>>> print "\tConsequences: ".join(",",@{$vf->consequence_type()}),"\n";
>>> if (1==1) {
>>> my $alleles = $vf->variation->get_all_Alleles();
>>> foreach my $allele (@{$alleles}) {
>>> next unless (defined $allele->population);
>>> my $allele_string = $allele->allele;
>>> my $frequency = $allele->frequency || 'NA';
>>> my $population_name = $allele->population->name;
>>> printf("\tAllele %s has frequency: %s in population %s.\n",
>>> $allele_string, $frequency, $po
>>> pulation_name);
>>> }
>>> }
>>> print "\n";
>>> }
>>>
>>>
>>>
>>>
>>> On Jul 7, 2016, at 12:51 PM, andrew126 at mac.com wrote:
>>>
>>> Hi Will,
>>>
>>> Yes, I can definitely share .. an example of a script that is throwing
>>> errors is in the original post at the start of the this thread.
>>>
>>> Many thanks,
>>>
>>> Andrew
>>>
>>> On Jul 7, 2016, at 11:57 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>
>>> Hi Andrew,
>>>
>>> Strange, are you able to share your test script?
>>>
>>> Another solution is to download the VCF files that are being opened over
>>> the FTP connection [1] and modifying the config file in
>>> ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json to
>>> point to the path where you downloaded the files.
>>>
>>> Cheers
>>>
>>> Will
>>>
>>> [1] : ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/ or for
>>> GRCh37
>>> ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/
>>>
>>>
>>> On 7 July 2016 at 13:49, <andrew126 at mac.com> wrote:
>>>
>>>> Hi Will,
>>>>
>>>> Thanks for the response.
>>>>
>>>> I've updated to the latest fixes, but I'm still getting these errors
>>>> using the same code.
>>>>
>>>> Is there anything else I can try?
>>>>
>>>> Thanks,
>>>>
>>>> Andrew
>>>>
>>>> andrew at ubuntu1404-64-ak:~/gte/src$ git ensembl --pull api
>>>> * Processing 'api'
>>>>
>>>> * Working with module 'ensembl'
>>>> * Performing pull
>>>> Already up-to-date.
>>>>
>>>> * Working with module 'ensembl-compara'
>>>> * Performing pull
>>>> Already up-to-date.
>>>>
>>>> * Working with module 'ensembl-funcgen'
>>>> * Performing pull
>>>> Already up-to-date.
>>>>
>>>> * Working with module 'ensembl-io'
>>>> * Performing pull
>>>> Already up-to-date.
>>>>
>>>> * Working with module 'ensembl-variation'
>>>> * Performing pull
>>>> Already up-to-date.
>>>>
>>>> perl tryit_crash.pl > tic.out &
>>>> [2] 3517
>>>> andrew at ubuntu1404-64-ak:~/gte$ UNIVERSAL->import is deprecated and
>>>> will be removed in a future perl at
>>>> /home/andrew/gte/src/bioperl-live/Bio/Tree/TreeFunctionsI.pm line 94.
>>>> Subroutine Tabix::tabix_open redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> Subroutine Tabix::tabix_close redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> Subroutine Tabix::tabix_query redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> Subroutine Tabix::tabix_read redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> Subroutine Tabix::tabix_getnames redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> Subroutine TabixIterator::tabix_iter_free redefined at
>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>> [kftp_connect_file] 530 You may not have more than 15 concurrent
>>>> connections at any time.
>>>> [kftp_connect_file] 530 You may not have more than 15 concurrent
>>>> connections at any time.
>>>> [main] fail to open the data file.
>>>> Tabix::tabix_query: t is not of type tabix_tPtr at
>>>> /home/andrew/gte/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line
>>>> 70.
>>>>
>>>>
>>>>
>>>> On Jul 7, 2016, at 6:35 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>>
>>>> Hi Andrew,
>>>>
>>>> We added a fix for this in the release/84 code ([1] if you're
>>>> interested) that limits the number of concurrent VCF connections to 2. If
>>>> you are on release/84, use git pull in the ensembl-variation directory to
>>>> get the latest fixes.
>>>>
>>>> If you are using an earlier version of the API, I'd suggest you update
>>>> to 84.
>>>>
>>>> Regards
>>>>
>>>> Will McLaren
>>>>
>>>> [1] :
>>>> https://github.com/Ensembl/ensembl-variation/commit/cd6813a66ca2cead9dc4da4e3a7bfa965b78f2ae
>>>>
>>>> On 6 July 2016 at 20:50, <andrew126 at mac.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm using API 84 on 64-bit Ubuntu.
>>>>>
>>>>> uname -a
>>>>> Linux ubuntu1404-64-ak 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan
>>>>> 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>> The below script reliably generates errors because of the number of
>>>>> concurrent connections. If get_all_Alleles() is not called, then no errors
>>>>> are experienced. I think other similar calls also generate these errors,
>>>>> but this is a simple example to get started.
>>>>>
>>>>> Posted below the script is an example of the error messages
>>>>> encountered.
>>>>>
>>>>> Is there a way to accomplish the same goal (summary of all alleles for
>>>>> each variant) without generating such errors?
>>>>>
>>>>> Please let me know if any other information would be useful.
>>>>>
>>>>> Thanks for any help,
>>>>>
>>>>> Andrew
>>>>>
>>>>>
>>>>> use strict;
>>>>> $|=1;
>>>>> use IPC::Run;
>>>>> use Bio::EnsEMBL::Registry;
>>>>> use Bio::EnsEMBL::ApiVersion;
>>>>> printf( "The API version used is %s\n", software_version() );
>>>>>
>>>>> my $registry = 'Bio::EnsEMBL::Registry';
>>>>> $registry->load_all();
>>>>> $registry->set_reconnect_when_lost();
>>>>> $registry->load_registry_from_db(
>>>>> -host => 'useastdb.ensembl.org',
>>>>> -user => 'anonymous'
>>>>> );
>>>>>
>>>>> my $gene_adaptor =
>>>>> $registry->get_adaptor('homo_sapiens','core','gene');
>>>>> my $slice_adaptor =
>>>>> $registry->get_adaptor('homo_sapiens','core','slice');
>>>>>
>>>>> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "4",
>>>>> 139000000, 139100000);
>>>>>
>>>>> print "Variation:\n";
>>>>>
>>>>> my $vf_adaptor = $registry->get_adaptor( 'human', 'variation',
>>>>> 'variationfeature' );
>>>>> $vf_adaptor->db->use_vcf(1);
>>>>> my $vars = $vf_adaptor->fetch_all_by_Slice($slice);
>>>>>
>>>>> foreach my $vf (@{$vars}){
>>>>> print "\t".$vf->variation_name(),"\n";
>>>>> print "\t".$vf->allele_string(),"\n";
>>>>> print "\tChromosome: ".$slice->seq_region_name."\n";
>>>>> print "\tStart-End:
>>>>> ".$vf->seq_region_start."-".$vf->seq_region_end."\n";
>>>>> print "\tConsequences: ".join(",",@{$vf->consequence_type()}),"\n";
>>>>> if (1==1) {
>>>>> my $alleles = $vf->variation->get_all_Alleles();
>>>>> foreach my $allele (@{$alleles}) {
>>>>> next unless (defined $allele->population);
>>>>> my $allele_string = $allele->allele;
>>>>> my $frequency = $allele->frequency || 'NA';
>>>>> my $population_name = $allele->population->name;
>>>>> printf("\tAllele %s has frequency: %s in population
>>>>> %s.\n", $allele_string, $frequency, $population_name);
>>>>> }
>>>>> }
>>>>> print "\n";
>>>>> }
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> andrew at ubuntu1404-64-ak:~/gte$ perl tryit_crash.pl > tic.out &
>>>>> [2] 3059
>>>>> andrew at ubuntu1404-64-ak:~/gte$ UNIVERSAL->import is deprecated and
>>>>> will be removed in a future perl at
>>>>> /home/andrew/gte/src/bioperl-live/Bio/Tree/TreeFunctionsI.pm line 94.
>>>>> Subroutine Tabix::tabix_open redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> Subroutine Tabix::tabix_close redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> Subroutine Tabix::tabix_query redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> Subroutine Tabix::tabix_read redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> Subroutine Tabix::tabix_getnames redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> Subroutine TabixIterator::tabix_iter_free redefined at
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
>>>>> [kftp_connect_file] 530 You may not have more than 15 concurrent
>>>>> connections at any time.
>>>>> [main] fail to open the data file.
>>>>> [kftp_connect_file] 530 You may not have more than 15 concurrent
>>>>> connections at any time.
>>>>> *** buffer overflow detected ***: perl terminated
>>>>> ======= Backtrace: =========
>>>>> /lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7f7fcd13138f]
>>>>> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f7fcd1c8c9c]
>>>>> /lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7f7fcd1c7b60]
>>>>> /lib/x86_64-linux-gnu/libc.so.6(+0x10abe7)[0x7f7fcd1c8be7]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xaebd)[0x7f7fc8011ebd]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xb0aa)[0x7f7fc80120aa]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(knet_read+0xb8)[0x7f7fc8012c18]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_read_block+0x165)[0x7f7fc8010c25]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_getline+0x37)[0x7f7fc8011cc7]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(ti_iter_read+0xd2)[0x7f7fc8010172]
>>>>>
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0x3368)[0x7f7fc800a368]
>>>>> /usr/lib/libperl.so.5.18(Perl_pp_entersub+0x596)[0x7f7fcd53c866]
>>>>> /usr/lib/libperl.so.5.18(Perl_runops_standard+0x16)[0x7f7fcd534e86]
>>>>> /usr/lib/libperl.so.5.18(perl_run+0x254)[0x7f7fcd4cd714]
>>>>> perl(main+0x149)[0x400dd9]
>>>>> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7fcd0dfec5]
>>>>> perl[0x400e11]
>>>>> ======= Memory map: ========
>>>>> 00400000-00402000 r-xp 00000000 fc:00 133596
>>>>> /usr/bin/perl
>>>>> 00601000-00602000 r--p 00001000 fc:00 133596
>>>>> /usr/bin/perl
>>>>> 00602000-00603000 rw-p 00002000 fc:00 133596
>>>>> /usr/bin/perl
>>>>> 01805000-061dc000 rw-p 00000000 00:00 0
>>>>> [heap]
>>>>> 7f7fc4000000-7f7fc4021000 rw-p 00000000 00:00 0
>>>>> 7f7fc4021000-7f7fc8000000 ---p 00000000 00:00 0
>>>>> 7f7fc8007000-7f7fc8015000 r-xp 00000000 fc:00 532847
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
>>>>> 7f7fc8015000-7f7fc8214000 ---p 0000e000 fc:00 532847
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
>>>>> 7f7fc8214000-7f7fc8215000 r--p 0000d000 fc:00 532847
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
>>>>> 7f7fc8215000-7f7fc8216000 rw-p 0000e000 fc:00 532847
>>>>> /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
>>>>> 7f7fc8216000-7f7fc822b000 r-xp 00000000 fc:00 260284
>>>>> /usr/lib/perl/5.18.2/auto/Storable/Storable.so
>>>>> 7f7fc822b000-7f7fc842a000 ---p 00015000 fc:00 260284
>>>>> /usr/lib/perl/5.18.2/auto/Storable/Storable.so
>>>>> 7f7fc842a000-7f7fc842b000 r--p 00014000 fc:00 260284
>>>>> /usr/lib/perl/5.18.2/auto/Storable/Storable.so
>>>>> 7f7fc842b000-7f7fc842c000 rw-p 00015000 fc:00 260284
>>>>> /usr/lib/perl/5.18.2/auto/Storable/Storable.so
>>>>> 7f7fc842c000-7f7fc842e000 r-xp 00000000 fc:00 260313
>>>>> /usr/lib/perl/5.18.2/auto/attributes/attributes.so
>>>>> 7f7fc842e000-7f7fc862d000 ---p 00002000 fc:00 260313
>>>>> /usr/lib/perl/5.18.2/auto/attributes/attributes.so
>>>>> 7f7fc862d000-7f7fc862e000 r--p 00001000 fc:00 260313
>>>>> /usr/lib/perl/5.18.2/auto/attributes/attributes.so
>>>>> 7f7fc862e000-7f7fc862f000 rw-p 00002000 fc:00 260313
>>>>> /usr/lib/perl/5.18.2/auto/attributes/attributes.so
>>>>> 7f7fc862f000-7f7fc863d000 r-xp 00000000 fc:00 311765
>>>>> /usr/lib/perl5/auto/JSON/XS/XS.so
>>>>> 7f7fc863d000-7f7fc883c000 ---p 0000e000 fc:00 311765
>>>>> /usr/lib/perl5/auto/JSON/XS/XS.so
>>>>> 7f7fc883c000-7f7fc883d000 r--p 0000d000 fc:00 311765
>>>>> /usr/lib/perl5/auto/JSON/XS/XS.so
>>>>> 7f7fc883d000-7f7fc883e000 rw-p 0000e000 fc:00 311765
>>>>> /usr/lib/perl5/auto/JSON/XS/XS.so
>>>>> 7f7fc883e000-7f7fc884c000 r-xp 00000000 fc:00 260173
>>>>> /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
>>>>> 7f7fc884c000-7f7fc8a4b000 ---p 0000e000 fc:00 260173
>>>>> /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
>>>>> 7f7fc8a4b000-7f7fc8a4c000 r--p 0000d000 fc:00 260173
>>>>> /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
>>>>> 7f7fc8a4c000-7f7fc8a4d000 rw-p 0000e000 fc:00 260173
>>>>> /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
>>>>> 7f7fc8a4d000-7f7fc8a53000 r-xp 00000000 fc:00 260228
>>>>> /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
>>>>> 7f7fc8a53000-7f7fc8c52000 ---p 00006000 fc:00 260228
>>>>> /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
>>>>> 7f7fc8c52000-7f7fc8c53000 r--p 00005000 fc:00 260228
>>>>> /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
>>>>> 7f7fc8c53000-7f7fc8c54000 rw-p 00006000 fc:00 260228
>>>>> /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
>>>>> 7f7fc8c54000-7f7fc8c5c000 r-xp 00000000 fc:00 260282
>>>>> /usr/lib/perl/5.18.2/auto/Socket/Socket.so
>>>>> 7f7fc8c5c000-7f7fc8e5c000 ---p 00008000 fc:00 260282
>>>>> /usr/lib/perl/5.18.2/auto/Socket/Socket.so
>>>>> 7f7fc8e5c000-7f7fc8e5e000 r--p 00008000 fc:00 260282
>>>>> /usr/lib/perl/5.18.2/auto/Socket/Socket.so
>>>>> 7f7fc8e5e000-7f7fc8e5f000 rw-p 0000a000 fc:00 260282
>>>>> /usr/lib/perl/5.18.2/auto/Socket/Socket.so
>>>>> 7f7fc8e5f000-7f7fc8e63000 r-xp 00000000 fc:00 260192
>>>>> /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
>>>>> 7f7fc8e63000-7f7fc9062000 ---p 00004000 fc:00 260192
>>>>> /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
>>>>> 7f7fc9062000-7f7fc9063000 r--p 00003000 fc:00 260192
>>>>> /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
>>>>> 7f7fc9063000-7f7fc9064000 rw-p 00004000 fc:00 260192
>>>>> /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
>>>>> 7f7fc9064000-7f7fc9066000 r-xp 00000000 fc:00 260176
>>>>> /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
>>>>> 7f7fc9066000-7f7fc9265000 ---p 00002000 fc:00 260176
>>>>> /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
>>>>> 7f7fc9265000-7f7fc9266000 r--p 00001000 fc:00 260176
>>>>> /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
>>>>> 7f7fc9266000-7f7fc9267000 rw-p 00002000 fc:00 260176
>>>>> /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
>>>>> 7f7fc9267000-7f7fc927e000 r-xp 00000000 fc:00 395859
>>>>> /lib/x86_64-linux-gnu/libresolv-2.19.so
>>>>> 7f7fc927e000-7f7fc947e000 ---p 00017000 fc:00 395859
>>>>> /lib/x86_64-linux-gnu/libresolv-2.19.so
>>>>> 7f7fc947e000-7f7fc947f000 r--p 00017000 fc:00 395859
>>>>> /lib/x86_64-linux-gnu/libresolv-2.19.so
>>>>> 7f7fc947f000-7f7fc9480000 rw-p 00018000 fc:00 395859
>>>>> /lib/x86_64-linux-gnu/libresolv-2.19.so
>>>>> 7f7fc9480000-7f7fc9482000 rw-p 00000000 00:00 0
>>>>> 7f7fc9482000-7f7fc9487000 r-xp 00000000 fc:00 395806
>>>>> /lib/x86_64-linux-gnu/libnss_dns-2.19.so
>>>>> 7f7fc9487000-7f7fc9686000 ---p 00005000 fc:00 395806
>>>>> /lib/x86_64-linux-gnu/libnss_dns-2.19.so
>>>>> 7f7fc9686000-7f7fc9687000 r--p 00004000 fc:00 395806
>>>>> /lib/x86_64-linux-gnu/libnss_dns-2.19.so
>>>>> 7f7fc9687000-7f7fc9688000 rw-p 00005000 fc:00 395806
>>>>> /lib/x86_64-linux-gnu/libnss_dns-2.19.so
>>>>> 7f7fc9688000-7f7fc968a000 r-xp 00000000 fc:00 395814
>>>>> /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
>>>>> 7f7fc968a000-7f7fc9889000 ---p 00002000 fc:00 395814
>>>>> /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
>>>>> 7f7fc9889000-7f7fc988a000 r--p 00001000 fc:00 395814
>>>>> /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
>>>>> 7f7fc988a000-7f7fc988b000 rw-p 00002000 fc:00 395814
>>>>> /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
>>>>> 7f7fc988b000-7f7fc9896000 r-xp 00000000 fc:00 395808
>>>>> /lib/x86_64-linux-gnu/libnss_files-2.19.so
>>>>> 7f7fc9896000-7f7fc9a95000 ---p 0000b000 fc:00 395808
>>>>> /lib/x86_64-linux-gnu/libnss_files-2.19.so
>>>>> 7f7fc9a95000-7f7fc9a96000 r--p 0000a000 fc:00 395808
>>>>> /lib/x86_64-linux-gnu/libnss_files-2.19.so
>>>>> 7f7fc9a96000-7f7fc9a97000 rw-p 0000b000 fc:00 395808
>>>>> /lib/x86_64-linux-gnu/libnss_files-2.19.so
>>>>> 7f7fc9a97000-7f7fc9aad000 r-xp 00000000 fc:00 395760
>>>>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>>>>> 7f7fc9aad000-7f7fc9cac000 ---p 00016000 fc:00 395760
>>>>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>>>>> 7f7fc9cac000-7f7fc9cad000 rw-p 00015000 fc:00 395760
>>>>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>>>>> 7f7fc9cad000-7f7fc9cae000 ---p 00000000 00:00 0
>>>>> 7f7fc9cae000-7f7fca4ae000 rw-p 00000000 00:00 0
>>>>> 7f7fca4ae000-7f7fca4c6000 r-xp 00000000 fc:00 395896
>>>>> /lib/x86_64-linux-gnu/libz.so.1.2.8
>>>>> 7f7fca4c6000-7f7fca6c5000 ---p 00018000 fc:00 395896
>>>>> /lib/x86_64-linux-gnu/libz.so.1.2.8
>>>>> 7f7fca6c5000-7f7fca6c6000 r--p 00017000 fc:00 395896
>>>>> /lib/x86_64-linux-gnu/libz.so.1.2.8
>>>>> 7f7fca6c6000-7f7fca6c7000 rw-p 00018000 fc:00 395896
>>>>> /lib/x86_64-linux-gnu/libz.so.1.2.8
>>>>> 7f7fca6c7000-7f7fca977000 r-xp 00000000 fc:00 183788
>>>>> /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
>>>>> 7f7fca977000-7f7fcab77000 ---p 002b0000 fc:00 183788
>>>>> /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
>>>>> 7f7fcab77000-7f7fcab7c000 r--p 002b0000 fc:00 183788
>>>>> /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
>>>>> 7f7fcab7c000-7f7fcabfa000 rw-p 002b5000 fc:00 183788
>>>>> /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
>>>>> 7f7fcabfa000-7f7fcabff000 rw-p 00000000 00:00 0
>>>>> 7f7fcabff000-7f7fcac19000 r-xp 00000000 fc:00 183957
>>>>> /usr/lib/perl5/auto/DBD/mysql/mysql.so
>>>>> 7f7fcac19000-7f7fcae19000 ---p 0001a000 fc:00 183957
>>>>> /usr/lib/perl5/auto/DBD/mysql/mysql.so
>>>>> 7f7fcae19000-7f7fcae1b000 r--p 0001a000 fc:00 183957
>>>>> /usr/lib/perl5/auto/DBD/mysql/mysql.so
>>>>> 7f7fcae1b000-7f7fcae1c000 rw-p 0001c000 fc:00 183957
>>>>> /usr/lib/perl5/auto/DBD/mysql/mysql.so
>>>>> 7f7fcae1c000-7f7fcae24000 r-xp 00000000 fc:00 260182
>>>>> /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
>>>>> 7f7fcae24000-7f7fcb023000 ---p 00008000 fc:00 260182
>>>>> /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
>>>>> 7f7fcb023000-7f7fcb024000 r--p 00007000 fc:00 260182
>>>>> /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
>>>>> 7f7fcb024000-7f7fcb025000 rw-p 00008000 fc:00 260182
>>>>> /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
>>>>> 7f7fcb025000-7f7fcb02c000 r-xp 00000000 fc:00 395861
>>>>> /lib/x86_64-linux-gnu/librt-2.19.so
>>>>> 7f7fcb02c000-7f7fcb22b000 ---p 00007000 fc:00 395861
>>>>> /lib/x86_64-linux-gnu/librt-2.19.so
>>>>> 7f7fcb22b000-7f7fcb22c000 r--p 00006000 fc:00 395861
>>>>> /lib/x86_64-linux-gnu/librt-2.19.so
>>>>> 7f7fcb22c000-7f7fcb22d000 rw-p 00007000 fc:00 395861
>>>>> /lib/x86_64-linux-gnu/librt-2.19.so
>>>>> 7f7fcb22d000-7f7fcb232000 r-xp 00000000 fc:00 260301
>>>>> /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
>>>>> 7f7fcb232000-7f7fcb431000 ---p 00005000 fc:00 260301
>>>>> /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
>>>>> 7f7fcb431000-7f7fcb432000 r--p 00004000 fc:00 260301
>>>>> /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
>>>>> 7f7fcb432000-7f7fcb433000 rw-p 00005000 fc:00 260301
>>>>> /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
>>>>> 7f7fcb433000-7f7fcb435000 r-xp 00000000 fc:00 260297
>>>>> /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
>>>>> 7f7fcb435000-7f7fcb634000 ---p 00002000 fc:00 260297
>>>>> /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
>>>>> 7f7fcb634000-7f7fcb635000 r--p 00001000 fc:00 260297
>>>>> /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
>>>>> 7f7fcb635000-7f7fcb636000 rw-p 00002000 fc:00 260297
>>>>> /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
>>>>> 7f7fcb636000-7f7fcb63b000 r-xp 00000000 fc:00 260251
>>>>> /usr/lib/perl/5.18.2/auto/List/Util/Util.so
>>>>> 7f7fcb63b000-7f7fcb83b000 ---p 00005000 fc:00 260251
>>>>> /usr/lib/perl/5.18.2/auto/List/Util/Util.so
>>>>> 7f7fcb83b000-7f7fcb83c000 r--p 00005000 fc:00 260251
>>>>> /usr/lib/perl/5.18.2/auto/List/Util/Util.so
>>>>> 7f7fcb83c000-7f7fcb83d000 rw-p 00006000 fc:00 260251
>>>>> /usr/lib/perl/5.18.2/auto/List/Util/Util.so
>>>>> 7f7fcb83d000-7f7fcb85b000 r-xp 00000000 fc:00 183894
>>>>> /usr/lib/perl5/auto/DBI/DBI.so
>>>>> 7f7fcb85b000-7f7fcba5a000 ---p 0001e000 fc:00 183894
>>>>> /usr/lib/perl5/auto/DBI/DBI.so
>>>>> 7f7fcba5a000-7f7fcba5b000 r--p 0001d000 fc:00 183894
>>>>> /usr/lib/perl5/auto/DBI/DBI.so
>>>>> 7f7fcba5b000-7f7fcba5c000 rw-p 0001e000 fc:00 183894
>>>>> /usr/lib/perl5/auto/DBI/DBI.so
>>>>> 7f7fcba5c000-7f7fcba60000 r-xp 00000000 fc:00 260245
>>>>> /usr/lib/perl/5.18.2/auto/IO/IO.so
>>>>> 7f7fcba60000-7f7fcbc5f000 ---p 00004000 fc:00 260245
>>>>> /usr/lib/perl/5.18.2/auto/IO/IO.so
>>>>> 7f7fcbc5f000-7f7fcbc60000 r--p 00003000 fc:00 260245
>>>>> /usr/lib/perl/5.18.2/auto/IO/IO.so
>>>>> 7f7fcbc60000-7f7fcbc61000 rw-p 00004000 fc:00 260245
>>>>> /usr/lib/perl/5.18.2/auto/IO/IO.so
>>>>> 7f7fcbc61000-7f7fcbc73000 r-xp 00000000 fc:00 260266
>>>>> /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
>>>>> 7f7fcbc73000-7f7fcbe72000 ---p 00012000 fc:00 260266
>>>>> /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
>>>>> 7f7fcbe72000-7f7fcbe75000 r--p 00011000 fc:00 260266
>>>>> /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
>>>>> 7f7fcbe75000-7f7fcbe76000 rw-p 00014000 fc:00 260266
>>>>> /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
>>>>> 7f7fcbe76000-7f7fcbe79000 r-xp 00000000 fc:00 260222
>>>>> /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
>>>>> 7f7fcbe79000-7f7fcc079000 ---p 00003000 fc:00 260222
>>>>> /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
>>>>> 7f7fcc079000-7f7fcc07a000 r--p 00003000 fc:00 260222
>>>>> /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
>>>>> 7f7fcc07a000-7f7fcc07b000 rw-p 00004000 fc:00 260222
>>>>> /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
>>>>> 7f7fcc07b000-7f7fcc75d000 r--p 00000000 fc:00 140924
>>>>> /usr/lib/locale/locale-archive
>>>>> 7f7fcc75d000-7f7fcc766000 r-xp 00000000 fc:00 395743
>>>>> /lib/x86_64-linux-gnu/libcrypt-2.19.so
>>>>> 7f7fcc766000-7f7fcc966000 ---p 00009000 fc:00 395743
>>>>> /lib/x86_64-linux-gnu/libcrypt-2.19.so
>>>>> 7f7fcc966000-7f7fcc967000 r--p 00009000 fc:00 395743
>>>>> /lib/x86_64-linux-gnu/libcrypt-2.19.so
>>>>> 7f7fcc967000-7f7fcc968000 rw-p 0000a000 fc:00 395743
>>>>> /lib/x86_64-linux-gnu/libcrypt-2.19.so
>>>>> [2]+ Aborted (core dumped) perl tryit_crash.pl >
>>>>> tic.out
>>>>>
>>>>>
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