I am trying add x11vnc as SMF service but cannot get service to start. I tried googling but couldn't find anything that could help me.
Here is the startup script
#!/sbin/sh
#
# Copyright (c) 1995, 1997-1999 by Sun Microsystems, Inc.
# All rights reserved.
#
#ident "#(#)x11vnc 1.14 06/11/17 SMI"
case "$1" in
'start')
#/usr/local/bin/x11vnc -geometry 1280x1024 -noshm -display :0 -ncache 10 -noshm -shared -forever -o /tmp/vnc_remote.log -bg
/usr/local/bin/x11vnc -unixpw -ncache 10 -display :0 -noshm -shared -forever -o /tmp/vnc_remote.log
;;
'stop')
/usr/bin/pkill -x -u 0 x11vnc
;;
*)
echo "Usage: $0 { start | stop }"
;;
esac
exit 0
and here is the manifest file
<?xml version='1.0'?>
<!DOCTYPE service_bundle SYSTEM '/usr/share/lib/xml/dtd/service_bundle.dtd.1'>
<service_bundle type='manifest' name='vnc'>
<service name='application/x11vnc' type='service' version='0'>
<create_default_instance enabled='true'/>
<single_instance/>
<dependency name='docusp' grouping='require_all' restart_on='none' type='service'>
<service_fmri value='svc:/milestone/multi-user-server:default'/>
</dependency>
<exec_method name='start' type='method' exec='/lib/svc/method/x11vnc' timeout_seconds='0'>
<method_context/>
</exec_method>
<exec_method name='stop' type='method' exec=':true' timeout_seconds='10'>
<method_context/>
</exec_method>
<stability value='Evolving' />
<property_group name='startd' type='framework'>
<propval name='ignore_error' type='astring' value='core,signal'/>
</property_group>
</service>
</service_bundle>
and the log file
Usage: /lib/svc/method/x11vnc { start | stop }
[ Nov 16 19:35:52 Method "start" exited with status 0 ]
[ Nov 16 19:35:52 Stopping because all processes in service exited. ]
[ Nov 16 19:35:52 Executing stop method (:kill) ]
[ Nov 16 19:35:52 Executing start method ("/lib/svc/method/x11vnc") ]
Usage: /lib/svc/method/x11vnc { start | stop }
[ Nov 16 19:35:52 Method "start" exited with status 0 ]
[ Nov 16 19:35:52 Stopping because all processes in service exited. ]
[ Nov 16 19:35:52 Executing stop method (:kill) ]
[ Nov 16 19:35:52 Executing start method ("/lib/svc/method/x11vnc") ]
Usage: /lib/svc/method/x11vnc { start | stop }
[ Nov 16 19:35:52 Method "start" exited with status 0 ]
[ Nov 16 19:35:52 Stopping because all processes in service exited. ]
[ Nov 16 19:35:52 Executing stop method (:kill) ]
[ Nov 16 19:35:52 Restarting too quickly, changing state to maintenance ]
Any Ideas?
You are missing to pass the "start" argument:
<exec_method name='start' type='method' exec='/lib/svc/method/x11vnc start' timeout_seconds='0'>
Related
I am following the tutorial in the documentation (https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html) and have been stuck on the "Step 4: Rule parameter" exercise. I would like to access a float from my config file using a wildcard in my params directive.
I seem to be getting the same error whenever I run snakemake -np in the command line:
InputFunctionException in line 46 of /mnt/c/Users/Matt/Desktop/snakemake-tutorial/Snakefile:
Error:
AttributeError: 'Wildcards' object has no attribute 'sample'
Wildcards:
Traceback:
File "/mnt/c/Users/Matt/Desktop/snakemake-tutorial/Snakefile", line 14, in get_bcftools_call_priors
This is my code so far
import time
configfile: "config.yaml"
rule all:
input:
"plots/quals.svg"
def get_bwa_map_input_fastqs(wildcards):
print(wildcards.__dict__, 1, time.time()) #I have this print as a check
return config["samples"][wildcards.sample]
def get_bcftools_call_priors(wildcards):
print(wildcards.__dict__, 2, time.time()) #I have this print as a check
return config["prior_mutation_rates"][wildcards.sample]
rule bwa_map:
input:
"data/genome.fa",
get_bwa_map_input_fastqs
#lambda wildcards: config["samples"][wildcards.sample]
output:
"mapped_reads/{sample}.bam"
params:
rg=r"#RG\tID:{sample}\tSM:{sample}"
threads: 2
shell:
"bwa mem -R '{params.rg}' -t {threads} {input} | samtools view -Sb - > {output}"
rule samtools_sort:
input:
"mapped_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam"
shell:
"samtools sort -T sorted_reads/{wildcards.sample} "
"-O bam {input} > {output}"
rule samtools_index:
input:
"sorted_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam.bai"
shell:
"samtools index {input}"
rule bcftools_call:
input:
fa="data/genome.fa",
bam=expand("sorted_reads/{sample}.bam", sample=config["samples"]),
bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"])
#prior=get_bcftools_call_priors
params:
prior=get_bcftools_call_priors
output:
"calls/all.vcf"
shell:
"samtools mpileup -g -f {input.fa} {input.bam} | "
"bcftools call -P {params.prior} -mv - > {output}"
rule plot_quals:
input:
"calls/all.vcf"
output:
"plots/quals.svg"
script:
"scripts/plot-quals.py"
and here is my config.yaml
samples:
A: data/samples/A.fastq
#B: data/samples/B.fastq
#C: data/samples/C.fastq
prior_mutation_rates:
A: 1.0e-4
#B: 1.0e-6
I don't understand why my input function call in bcftools_call says that the wildcards object is empty of attributes, yet an almost identical function call in bwa_map has the attribute sample that I want. From the documentation it seems like the wildcards would be propogated before anything is run, so why is it missing?
This is the full output of the commandline call snakemake -np:
{'_names': {'sample': (0, None)}, '_allowed_overrides': ['index', 'sort'], 'index': functools.partial(<function Namedlist._used_attribute at 0x7f91b1a58f70>, _name='index'), 'sort': functools.partial(<function Namedlist._used_attribute at 0x7f91b1a58f70>, _name='sort'), 'sample': 'A'} 1 1628877061.8831172
Job stats:
job count min threads max threads
-------------- ------- ------------- -------------
all 1 1 1
bcftools_call 1 1 1
bwa_map 1 1 1
plot_quals 1 1 1
samtools_index 1 1 1
samtools_sort 1 1 1
total 6 1 1
[Fri Aug 13 10:51:01 2021]
rule bwa_map:
input: data/genome.fa, data/samples/A.fastq
output: mapped_reads/A.bam
jobid: 4
wildcards: sample=A
resources: tmpdir=/tmp
bwa mem -R '#RG\tID:A\tSM:A' -t 1 data/genome.fa data/samples/A.fastq | samtools view -Sb - > mapped_reads/A.bam
[Fri Aug 13 10:51:01 2021]
rule samtools_sort:
input: mapped_reads/A.bam
output: sorted_reads/A.bam
jobid: 3
wildcards: sample=A
resources: tmpdir=/tmp
samtools sort -T sorted_reads/A -O bam mapped_reads/A.bam > sorted_reads/A.bam
[Fri Aug 13 10:51:01 2021]
rule samtools_index:
input: sorted_reads/A.bam
output: sorted_reads/A.bam.bai
jobid: 5
wildcards: sample=A
resources: tmpdir=/tmp
samtools index sorted_reads/A.bam
[Fri Aug 13 10:51:01 2021]
rule bcftools_call:
input: data/genome.fa, sorted_reads/A.bam, sorted_reads/A.bam.bai
output: calls/all.vcf
jobid: 2
resources: tmpdir=/tmp
{'_names': {}, '_allowed_overrides': ['index', 'sort'], 'index': functools.partial(<function Namedlist._used_attribute at 0x7f91b1a58f70>, _name='index'), 'sort': functools.partial(<function Namedlist._used_attribute at 0x7f91b1a58f70>, _name='sort')} 2 1628877061.927639
InputFunctionException in line 46 of /mnt/c/Users/Matt/Desktop/snakemake-tutorial/Snakefile:
Error:
AttributeError: 'Wildcards' object has no attribute 'sample'
Wildcards:
Traceback:
File "/mnt/c/Users/Matt/Desktop/snakemake-tutorial/Snakefile", line 14, in get_bcftools_call_priors
If anyone knows what is going wrong I would really appreciate an explaination. Also if there is a better way of getting information out of the config.yaml into the different directives, I would gladly appreciate those tips.
Edit:
I have searched around the internet quite a bit, but have yet to understand this issue.
Wildcards for each rule are based on that rule's output file(s). The rule bcftools_call has one output file (calls/all.vcf), which has no wildcards. Because of this, when get_bcftools_call_priors is called, it throws an exception when it tries to access the unset wildcards.sample attribute.
You should probably set a global prior_mutation_rate in your config file and then access that in the bcftools_call rule:
rule bcftools_call:
...
params:
prior=config["prior_mutation_rate"],
I installed on CentOs successfully ever. However, here is another CentOs I used, and it failed to stared rabbitMq.
My erlang from here.
[rabbitmq-erlang]
name=rabbitmq-erlang
baseurl=https://dl.bintray.com/rabbitmq/rpm/erlang/20/el/7
gpgcheck=1
gpgkey=https://dl.bintray.com/rabbitmq/Keys/rabbitmq-release-signing-key.asc
repo_gpgcheck=0
enabled=1
this is my erl_crash.dump.
erl_crash_dump:0.5
Sat Jun 23 09:17:30 2018
Slogan: init terminating in do_boot ({error,{no such file or directory,asn1.app}})
System version: Erlang/OTP 20 [erts-9.3.3] [source] [64-bit] [smp:24:24] [ds:24:24:10] [async-threads:384] [hipe] [kernel-poll:true]
Compiled: Tue Jun 19 22:25:03 2018
Taints: erl_tracer,zlib
Atoms: 14794
Calling Thread: scheduler:2
=scheduler:1
Scheduler Sleep Info Flags: SLEEPING | TSE_SLEEPING | WAITING
Scheduler Sleep Info Aux Work:
Current Port:
Run Queue Max Length: 0
Run Queue High Length: 0
Run Queue Normal Length: 0
Run Queue Low Length: 0
Run Queue Port Length: 0
Run Queue Flags: OUT_OF_WORK | HALFTIME_OUT_OF_WORK
Current Process:
=scheduler:2
Scheduler Sleep Info Flags:
Scheduler Sleep Info Aux Work: THR_PRGR_LATER_OP
Current Port:
Run Queue Max Length: 0
Run Queue High Length: 0
Run Queue Normal Length: 0
Run Queue Low Length: 0
Run Queue Port Length: 0
Run Queue Flags: OUT_OF_WORK | HALFTIME_OUT_OF_WORK | NONEMPTY | EXEC
Current Process: <0.0.0>
Current Process State: Running
Current Process Internal State: ACT_PRIO_NORMAL | USR_PRIO_NORMAL | PRQ_PRIO_NORMAL | ACTIVE | RUNNING | TRAP_EXIT | ON_HEAP_MSGQ
Current Process Program counter: 0x00007fbd81fa59c0 (init:boot_loop/2 + 64)
Current Process CP: 0x0000000000000000 (invalid)
how to identify this problem ? Thank you.
E0302 03:12:50.399718 23466 net.cpp:785] [Backward] All net params (data, diff): L1 norm = (13513.7, 65688.6); L2 norm = (23.9842, 295.159)
F0302 03:14:40.549015 23466 syncedmem.hpp:31] Check failed: error == cudaSuccess (29 vs. 0) driver shutting down
*** Check failure stack trace: ***
------------------------------------------------------------------------
abort() detected at Fri Mar 2 03:14:40 2018
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Current Graphics Driver: Unknown hardware
Current Visual : 0x21 (class 4, depth 24)
Default Encoding : UTF-8
Deployed : false
GNU C Library : 2.23 stable
Host Name : lly
MATLAB Architecture : glnxa64
MATLAB Entitlement ID: 6257193
MATLAB Root : /usr/local/MATLAB/R2016b
MATLAB Version : 9.1.0.441655 (R2016b)
OpenGL : hardware
Operating System : Linux 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64
Processor ID : x86 Family 6 Model 158 Stepping 9, GenuineIntel
Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : The X.Org Foundation (11905000), display :0
Fault Count: 1
Abnormal termination:
abort()
Register State (from fault):
RAX = 0000000000000000 RBX = 00007fb35b643420
RCX = 00007fb4b71e9428 RDX = 0000000000000006
RSP = 00007fb49a94d008 RBP = 00007fb49a94d2e0
RSI = 0000000000005baa RDI = 0000000000005b76
R8 = 0000000000000081 R9 = 00007fb35b643440
R10 = 0000000000000008 R11 = 0000000000000202
R12 = 00007fb35b643480 R13 = 0000000000000072
R14 = 00007fb35b643420 R15 = 00007fb35b64ade0
RIP = 00007fb4b71e9428 EFL = 0000000000000202
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007fb4b71e9428 /lib/x86_64-linux-gnu/libc.so.6+00218152 gsignal+00000056
[ 1] 0x00007fb4b71eb02a /lib/x86_64-linux-gnu/libc.so.6+00225322 abort+00000362
[ 2] 0x00007fb35b42ee49 /usr/lib/x86_64-linux-gnu/libglog.so.0+00040521
[ 3] 0x00007fb35b4305cd /usr/lib/x86_64-linux-gnu/libglog.so.0+00046541
[ 4] 0x00007fb35b432433 /usr/lib/x86_64-linux-gnu/libglog.so.0+00054323 _ZN6google10LogMessage9SendToLogEv+00000643
[ 5] 0x00007fb35b43015b /usr/lib/x86_64-linux-gnu/libglog.so.0+00045403 _ZN6google10LogMessage5FlushEv+00000187
[ 6] 0x00007fb35b432e1e /usr/lib/x86_64-linux-gnu/libglog.so.0+00056862 _ZN6google15LogMessageFatalD2Ev+00000014
[ 7] 0x00007fb35b9fe8d0 /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+01329360
[ 8] 0x00007fb35b9c9512 /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+01111314
[ 9] 0x00007fb35b99bfca /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+00925642
[ 10] 0x00007fb35b99c3dd /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+00926685
[ 11] 0x00007fb35bbabae5 /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+03087077
[ 12] 0x00007fb35b91a01f /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+00393247
[ 13] 0x00007fb35b91a19a /home/lly/work/caffe-ssd/matlab/+caffe/private/caffe_.mexa64+00393626
[ 14] 0x00007fb4b71edff8 /lib/x86_64-linux-gnu/libc.so.6+00237560
[ 15] 0x00007fb4b71ee045 /lib/x86_64-linux-gnu/libc.so.6+00237637
[ 16] 0x00007fb4a6f047c0 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00767936
[ 17] 0x00007fb4a6f03011 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00761873
[ 18] 0x00007fb4a6bb9cfe /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_dispatcher.so+00437502
[ 19] 0x00007fb4a6ba0878 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_dispatcher.so+00333944 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000616
[ 20] 0x00007fb499146a38 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcos_impl.so+02771512
[ 21] 0x00007fb4a6bf5bd5 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_dispatcher.so+00682965
[ 22] 0x00007fb4a6bb9cfe /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_dispatcher.so+00437502
[ 23] 0x00007fb4a6ba0878 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_dispatcher.so+00333944 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000616
[ 24] 0x00007fb4a3b2a9b4 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+12614068
[ 25] 0x00007fb4a3b2aa50 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+12614224
[ 26] 0x00007fb4a3909306 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+10380038
[ 27] 0x00007fb4a3909785 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+10381189
[ 28] 0x00007fb4a3989cc8 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+10906824
[ 29] 0x00007fb4a398ba2a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_lxe.so+10914346
[ 30] 0x00007fb4a632aee0 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwm_interpreter.so+02445024 _Z44inCallFcnWithTrapInDesiredWSAndPublishEventsiPP11mxArray_tagiS1_PKcbP15inWorkSpace_tag+00000080
[ 31] 0x00007fb4a766a77a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00690042 _ZN3iqm15BaseFEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000522
[ 32] 0x00007fb4803cea3f /usr/local/MATLAB/R2016b/bin/glnxa64/libnativejmi.so+00862783 _ZN9nativejmi14JmiFEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000319
[ 33] 0x00007fb4803f1bd5 /usr/local/MATLAB/R2016b/bin/glnxa64/libnativejmi.so+01006549 _ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN9nativejmi14JmiFEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000741
[ 34] 0x00007fb4a7660a0a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00649738
[ 35] 0x00007fb4a764ceb2 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00569010
[ 36] 0x00007fb4a5ea805a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwbridge.so+00159834
[ 37] 0x00007fb4a5ea8617 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwbridge.so+00161303
[ 38] 0x00007fb4a5eaf519 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwbridge.so+00189721
[ 39] 0x00007fb4a5eaf614 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwbridge.so+00189972
[ 40] 0x00007fb4a5eaffa9 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwbridge.so+00192425 _Z8mnParserv+00000617
[ 41] 0x00007fb4a6ecc243 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00537155
[ 42] 0x00007fb4a6ece1ce /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00545230
[ 43] 0x00007fb4a6ece849 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00546889 _ZN5boost6detail17task_shared_stateINS_3_bi6bind_tIvPFvRKNS_8functionIFvvEEEENS2_5list1INS2_5valueIS6_EEEEEEvE6do_runEv+00000025
[ 44] 0x00007fb4a6ecd236 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00541238
[ 45] 0x00007fb4a7694b49 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00863049
[ 46] 0x00007fb4a768151c /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00783644 _ZN5boost6detail8function21function_obj_invoker0ISt8functionIFNS_3anyEvEES4_E6invokeERNS1_15function_bufferE+00000028
[ 47] 0x00007fb4a76811fc /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00782844 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+00000428
[ 48] 0x00007fb4a7660a0a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00649738
[ 49] 0x00007fb4a764c690 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00566928
[ 50] 0x00007fb4a764f048 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwiqm.so+00577608
[ 51] 0x00007fb4b895340a /usr/local/MATLAB/R2016b/bin/glnxa64/libmwservices.so+02634762
[ 52] 0x00007fb4b89549af /usr/local/MATLAB/R2016b/bin/glnxa64/libmwservices.so+02640303
[ 53] 0x00007fb4b89550e6 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwservices.so+02642150 _Z25svWS_ProcessPendingEventsiib+00000102
[ 54] 0x00007fb4a6ecc8c6 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00538822
[ 55] 0x00007fb4a6eccc42 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00539714
[ 56] 0x00007fb4a6eba8d6 /usr/local/MATLAB/R2016b/bin/glnxa64/libmwmcr.so+00465110
[ 57] 0x00007fb4b75856ba /lib/x86_64-linux-gnu/libpthread.so.0+00030394
[ 58] 0x00007fb4b72bb41d /lib/x86_64-linux-gnu/libc.so.6+01078301 clone+00000109
[ 59] 0x0000000000000000 <unknown-module>+00000000
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /home/lly/matlab_crash_dump.23414-1 **
MATLAB is exiting because of fatal error
Killed
Here is my hardware information:
ubuntu 16.04
gtx1070
cdua8.0
cudnn5.1
NVIDIA Drivers: NVIDIA-Linux-x86_64-384.111.run
MATLAB2016b
Any idea on how to solve this? Thank you very much!
Here is my compile caffe process:
Because MATLAB library files and Ubuntu system library files conflict, first i backuped the MATLAB file, and then added the system files to the environment variables, so that the system will use the system's default dynamic file.
①Rename libstdc++.so.6 to libstdc++.so.6_back in the directory of /usr/local/MATLAB/R2016b/sys/os/glnxa64
②execute sudo make matcaffe -j8 which is successful.
③execute sudo make mattest -j8 get this wrong information:
Invalid MEX-file
'/home/lly/work/caffe/matlab/+caffe/private/caffe_.mexa64':
/home/lly/work/caffe/matlab/+caffe/private/caffe_.mexa64: undefined
symbol:
_ZN2cv8imencodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11_InputArrayERSt6vectorIhSaIhEERKSB_IiSaIiEE.
Error in caffe.set_mode_cpu (line 5)
caffe_('set_mode_cpu');
Error in caffe.run_tests (line 6)
caffe.set_mode_cpu();
④Then, I deleted six MATLAB files in directory /usr/local/MATLAB/R2016b/bin/glnxa64, in order to solve this problem.But finally got the matlab crash problem.
sudo mv libopencv_core.so.2.4 libopencv_core.so.2.4.bak
sudo mv libopencv_core.so.2.4.9 libopencv_core.so.2.4.9.bak
sudo mv libopencv_highgui.so.2.4 libopencv_highgui.so.2.4.bak
sudo mv libopencv_highgui.so.2.4.9 libopencv_highgui.so.2.4.9.bak
sudo mv libopencv_imgproc.so.2.4 libopencv_imgproc.so.2.4.bak
sudo mv libopencv_imgproc.so.2.4.9 libopencv_imgproc.so.2.4.9.bak
Look at the following two things in your log.
Current Graphics Driver: Unknown hardware
OpenGL : hardware
The first one needs to be populated by your graphics card driver information. That is not happening.
Perform the following test:
Put OpenGL to be Software. Check that it has been moved to software
by typing: h = opengl('info')
Check that the current graphics driver field is populated with whatever software driver you have.
Make sure to save these settings.
Restart the Matlab.
Reconfirm the settings and make sure opengl is to software.
Replicate the crash.
Share the Log.
After this you can try running the memory diagnostic on your System Memory and Graphics Card.
I had faced a similar issue and it turned out that there was a problem in my System Memory and Graphics card.
But that you will come to know after the log report is generated.
I have two simple indexes:
First, 01.conf:
searchd
{
listen = 9301
listen = 9401:mysql41
pid_file = /var/run/sphinxsearch/searchd01.pid
log = /var/log/sphinxsearch/searchd01.log
query_log = /var/log/sphinxsearch/query01.log
binlog_path = /var/lib/sphinxsearch/data/test/01
}
source base
{
type = mysql
sql_host = localhost
sql_db = test
sql_user = root
sql_pass = toor
sql_query_pre = SET NAMES utf8
sql_attr_uint = group_id
}
source test : base
{
sql_query = \
SELECT id, group_id, UNIX_TIMESTAMP(date_added) AS date_added, title, content \
FROM documents WHERE id % 2 = 0
}
index test
{
source = test
path = /var/lib/sphinxsearch/data/test/01
}
Second looks like first but with "02" instead "01" in filename and inside.
And distributed index in 00.conf:
searchd
{
listen = 9305
listen = 9405:mysql41
pid_file = /var/run/sphinxsearch/searchd00.pid
log = /var/log/sphinxsearch/searchd00.log
query_log = /var/log/sphinxsearch/query00.log
binlog_path = /var/lib/sphinxsearch/data/test
}
index test
{
type = distributed
agent = 127.0.0.1:9301:test
agent = 127.0.0.1:9302:test
}
And I try to use distributed index:
sudo searchd --config /etc/sphinxsearch/d/00.conf --stop
sudo searchd --config /etc/sphinxsearch/d/01.conf --stop
sudo searchd --config /etc/sphinxsearch/d/02.conf --stop
sudo searchd --config /etc/sphinxsearch/d/01.conf
sudo searchd --config /etc/sphinxsearch/d/02.conf
sudo indexer --all --rotate --config /etc/sphinxsearch/d/01.conf
sudo indexer --all --rotate --config /etc/sphinxsearch/d/02.conf
sudo searchd --config /etc/sphinxsearch/d/00.conf
Unfortunately I obtain next output:
...
using config file '/etc/sphinxsearch/d/00.conf'...
listening on all interfaces, port=9305
listening on all interfaces, port=9405
precached 0 indexes in 0.000 sec
Why?
And when I try to search something with distributed index (9305):
no enabled local indexes to search.
And mysql indexes are works perfectly if I use them with port 9301 and 9302 respectively. But searching in distributed index returns nothing.
UPDATE
# tail /var/log/sphinxsearch/searchd00.log
[Thu Sep 29 23:43:04.599 2016] [ 2353] binlog: finished replaying /var/lib/sphinxsearch/data/test/binlog.001; 0.0 MB in 0.000 sec
[Thu Sep 29 23:43:04.599 2016] [ 2353] binlog: finished replaying total 4 in 0.000 sec
[Thu Sep 29 23:43:04.599 2016] [ 2353] accepting connections
[Thu Sep 29 23:43:24.336 2016] [ 2353] caught SIGTERM, shutting down
[Thu Sep 29 23:43:24.472 2016] [ 2353] shutdown complete
[Thu Sep 29 23:43:24.473 2016] [ 2352] watchdog: main process 2353 exited cleanly (exit code 0), shutting down
[Thu Sep 29 23:43:24.634 2016] [ 2404] watchdog: main process 2405 forked ok
[Thu Sep 29 23:43:24.635 2016] [ 2405] listening on all interfaces, port=9305
[Thu Sep 29 23:43:24.635 2016] [ 2405] listening on all interfaces, port=9405
[Thu Sep 29 23:43:24.636 2016] [ 2405] accepting connections
UPDATE2
Hmm... It seems what problem in querying data from Sphinx. Also I renamed distributed index into test1. Next code works well.
# mysql -h 127.0.0.1 -P 9405
mysql> select * from test1 where match ('one|two');
+------+----------+
| id | group_id |
+------+----------+
| 1 | 1 |
| 2 | 1 |
+------+----------+
2 rows in set (0,00 sec)
I think what problem was in old version of sphinxapi.php what I used.
precached 0 indexes in 0.000 sec
Well that it self, is normal. There are no local indexes to 'precache'. A distributed index has no index files to 'load' or (pre)cache.
... but searchd should still be running at the end of that. I think searchd should start up ok.
Try also checking
/var/log/sphinxsearch/searchd00.log
might have some more.
Although I suppose its possible sphinx will not startup without any real indexes (ie cant have JUST distributed index), so could just add a fake index to that config.
I cannot seem to build perl 5.6.2 in Cygwin 1.7.11.
Here are the steps I am following to do it so far.
Download perl 5.6.2 source from website and untar to some folder "perl-5.6.2"
cd perl-5.6.2/bld
sh ../Configure -des -Dmksymlinks -Dprefix=/common/ndd/perl/5.6.2 -DDEBUGGING 2>&1
make 2>&1
make install 2>&1
Here are the logs from this:
http://pastebin.com/pqLg4S7z
What happens is make creates "perl-5.6.2/bld/perl.exe" and this file generates an abort signal every time.
Here is the backtrace from running gdb on it. (Note: I configured with -DDEBUGGING so all the gcc debug flags should be enabled.)
(gdb) run
Starting program: /openlogic/build/work/perl-5.6.2/bld/perl.exe
[New Thread 3348.0xf54]
[New Thread 3348.0x48c]
Program received signal SIGABRT, Aborted.
0x00000000 in ?? ()
(gdb) backtrace
#0 0x00000000 in ?? ()
#1 0x7792f8b1 in ntdll!RtlUpdateClonedSRWLock ()
from /cygdrive/c/Windows/system32/ntdll.dll
#2 0x757f0a91 in WaitForSingleObjectEx ()
from /cygdrive/c/Windows/syswow64/KERNELBASE.dll
#3 0x000000a8 in ?? ()
#4 0x00000000 in ?? ()
(gdb) quit
Here id the ldd.exe command ran on perl.exe
$ ldd /ndipiazza/build/work/perl-5.6.2/bld/perl.exe
ntdll.dll => /cygdrive/c/Windows/SysWOW64/ntdll.dll (0x77910000)
kernel32.dll => /cygdrive/c/Windows/syswow64/kernel32.dll (0x75cb0000)
KERNELBASE.dll => /cygdrive/c/Windows/syswow64/KERNELBASE.dll (0x757e0000)
libperl5_6_2.dll => /ndipiazza/build/work/perl-5.6.2/bld/libperl5_6_2.dll (0x66140000)
cygcrypt-0.dll => /usr/bin/cygcrypt-0.dll (0x67db0000)
cygwin1.dll => /usr/bin/cygwin1.dll (0x61000000)
??? => ??? (0x570000)
Can anyone see why I would be getting this sigabrt?
EDIT: here is a link to a discussion going on in Cygwin mailing list: http://cygwin.com/ml/cygwin/2012-07/msg00368.html
5.6 is outdated for your build environment. Maintenance patches exist.
I recommend to install perlbrew and patchperl:
$ perlbrew install-patchperl
which will DTRT.
This question is above my pay grade and this is a shot in the dark, but the two things I remember that ruin a perl5.6.2 build on Cygwin are
spaces in the $PATH (e.g. /cygdrive/c/Program Files/BlahBlahBlah)
configure script unable to determine the signal names
Check your config.sh script and see whether it contains lines like
sig_count='1'
sig_name='ZERO '
sig_name_init='"ZERO", 0'
sig_num='0 '
sig_num_init='0, 0'
You want it to say something like
sig_count='33'
sig_name='ZERO HUP INT QUIT ILL TRAP ABRT EMT FPE KILL BUS SEGV SYS PIPE ALRM TERM URG STOP TSTP CONT CHLD TTIN TTOU IO XCPU XFSZ VTALRM PROF WINCH LOST USR1 USR2 RTMAX CLD POLL PWR RTMIN '
sig_name_init='"ZERO", "HUP", "INT", "QUIT", "ILL", "TRAP", "ABRT", "EMT", "FPE", "KILL", "BUS", "SEGV", "SYS", "PIPE", "ALRM", "TERM", "URG", "STOP", "TSTP", "CONT", "CHLD", "TTIN", "TTOU", "IO", "XCPU", "XFSZ", "VTALRM", "PROF", "WINCH", "LOST", "USR1", "USR2", "RTMAX", "CLD", "POLL", "PWR", "RTMIN", 0'
sig_num='0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 20 23 29 32 '
sig_num_init='0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 20, 23, 29, 32, 0'
(I copied these values from a config.sh from a build for a newer version of Perl. The values you need may vary slightly)
I figured it out. Perl 5.6.2 tries to use it's own malloc. This is incompatible with Cygwin's malloc.
I was given some help on Cygwin mailing list to fix this: http://cygwin.com/ml/cygwin/2012-07/msg00380.html
Bottom line, add -Dusemymalloc=n to the sh ./Configure arguments.
Then it works.