Stream: committers/notification
Topic: Timing out
Mark Kramer (Feb 17 2020 at 23:38):
Can anyone suggest something to help this build go through? I haven't had problems before, but now the terminology server appears to be timing out.
INFO:root:about to clone!
DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-mCODE-ig --branch master repo
DEBUG:root:Time to deadline 3479.997499 seconds
Cloning into 'repo'...
DEBUG:root:running: wget -q https://github.com/FHIR/latest-ig-publisher/raw/master/org.hl7.fhir.publisher.jar -O publisher.jar
DEBUG:root:Time to deadline 3478.178296 seconds
DEBUG:root:running: java -Xms14000m -Xmx14000m -jar ../publisher.jar -ig ig.json -auto-ig-build -target https://build.fhir.org/ig/HL7/fhir-mCODE-ig/ -out /scratch/ig-build-temp-EW0637/repo
DEBUG:root:Time to deadline 3476.005458 seconds
FHIR IG Publisher Version 1.0.64-SNAPSHOT (Git# 2bbc3a2a5ac3). Built 2020-02-13T21:52:04.259+11:00 (4 days old)
Detected Java version: 12.0.1 from /usr/java/openjdk-12 on amd64 (64bit). 13533MB available
Parameters: -ig ig.json -auto-ig-build -target https://build.fhir.org/ig/HL7/fhir-mCODE-ig/ -out /scratch/ig-build-temp-EW0637/repo
dir = /scratch/ig-build-temp-EW0637/repo, path = /usr/local/rvm/bin:/usr/local/rvm/rubies/ruby-2.5.1/bin:/usr/java/openjdk-12/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Run time = Monday, February 17, 2020 at 10:35:25 PM Coordinated Universal Time (2020-02-17T22:35:25Z)
Package Cache: var/lib/.fhir/packages (00:00.0025)
Contacting Build Server... (00:00.0029)
... done (00:00.0929)
Load Template from hl7.base.template#current (00:01.0708)
Installing hl7.base.template#current to the package cache
Fetching:
Installing: done.
Load Template from fhir.base.template#current (00:01.0761)
Installing fhir.base.template#current to the package cache
Fetching:.
Installing: . done.
onLoad.findSpreadsheets:
onLoad.updateIg:
[xslt] Processing /scratch/ig-build-temp-EW0637/repo/template/onLoad-ig-working.xml to /scratch/ig-build-temp-EW0637/repo/template/onLoad-ig-updated.xml
[xslt] Loading stylesheet /scratch/ig-build-temp-EW0637/repo/template/scripts/onLoad.xslt
onLoad.extend:
onLoad:
Root directory: /scratch/ig-build-temp-EW0637/repo (00:03.0442)
Core Package hl7.fhir.r4.core#4.0.1
Installing hl7.fhir.r4.core#4.0.1 to the package cache
Fetching:..............................................................................................
Installing: .............................................................................................. done.
Terminology Cache is at /scratch/ig-build-temp-EW0637/repo/input-cache/txcache. Trimming now (00:11.0764)
Connect to Terminology Server at http://tx.fhir.org (00:12.0086)
Installing hl7.fhir.pubpack#0.0.3 to the package cache
Fetching:.......
Installing: ....... done.
Load Package hl7.fhir.pubpack#0.0.3
Installing hl7.fhir.xver-extensions#0.0.1 to the package cache
Fetching:
Installing: done.
Load Package hl7.fhir.xver-extensions#0.0.1
Dependency 'hl7.fhir.us.core' has no id, so can't be referred to in markdown in the IG (00:13.0375)
Installing hl7.fhir.us.core#3.1.0 to the package cache
Fetching:.....
Installing: ..... done.
Initialization complete (00:14.0558)
Load Content (00:14.0558)
Processing Conformance Resources (00:15.0334)
Terminology server: Check for supported code systems for http://snomed.info/sct (00:17.0517)
DEBUG:root:
*** Timeout -- deadline reached
Mark Kramer (Feb 17 2020 at 23:53):
Well, it seems to have gone through with time outs only on a certain few elements. I don't know what to make of the errors (message truncated for length).
NFO:root:about to clone!
DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-mCODE-ig --branch master repo
DEBUG:root:Time to deadline 3479.998003 seconds
Cloning into 'repo'...
DEBUG:root:running: wget -q https://github.com/FHIR/latest-ig-publisher/raw/master/org.hl7.fhir.publisher.jar -O publisher.jar
DEBUG:root:Time to deadline 3478.128505 seconds
DEBUG:root:running: java -Xms14000m -Xmx14000m -jar ../publisher.jar -ig ig.json -auto-ig-build -target https://build.fhir.org/ig/HL7/fhir-mCODE-ig/ -out /scratch/ig-build-temp-FXW5GK/repo
DEBUG:root:Time to deadline 3476.858675 seconds
FHIR IG Publisher Version 1.0.64-SNAPSHOT (Git# 2bbc3a2a5ac3). Built 2020-02-13T21:52:04.259+11:00 (4 days old)
Detected Java version: 12.0.1 from /usr/java/openjdk-12 on amd64 (64bit). 13533MB available
Parameters: -ig ig.json -auto-ig-build -target https://build.fhir.org/ig/HL7/fhir-mCODE-ig/ -out /scratch/ig-build-temp-FXW5GK/repo
dir = /scratch/ig-build-temp-FXW5GK/repo, path = /usr/local/rvm/bin:/usr/local/rvm/rubies/ruby-2.5.1/bin:/usr/java/openjdk-12/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Run time = Monday, February 17, 2020 at 11:02:13 PM Coordinated Universal Time (2020-02-17T23:02:13Z)
Package Cache: var/lib/.fhir/packages (00:00.0023)
Contacting Build Server... (00:00.0025)
... done (00:00.0860)
Load Template from hl7.base.template#current (00:01.0617)
Installing hl7.base.template#current to the package cache
Fetching:
Installing: done.
Load Template from fhir.base.template#current (00:01.0663)
Installing fhir.base.template#current to the package cache
Fetching:.
Installing: . done.
onLoad.findSpreadsheets:
onLoad.updateIg:
[xslt] Processing /scratch/ig-build-temp-FXW5GK/repo/template/onLoad-ig-working.xml to /scratch/ig-build-temp-FXW5GK/repo/template/onLoad-ig-updated.xml
[xslt] Loading stylesheet /scratch/ig-build-temp-FXW5GK/repo/template/scripts/onLoad.xslt
onLoad.extend:
onLoad:
Root directory: /scratch/ig-build-temp-FXW5GK/repo (00:03.0324)
Core Package hl7.fhir.r4.core#4.0.1
Installing hl7.fhir.r4.core#4.0.1 to the package cache
Fetching:..............................................................................................
Installing: .............................................................................................. done.
Terminology Cache is at /scratch/ig-build-temp-FXW5GK/repo/input-cache/txcache. Trimming now (00:12.0025)
Connect to Terminology Server at http://tx.fhir.org (00:12.0425)
Installing hl7.fhir.pubpack#0.0.3 to the package cache
Fetching:.......
Installing: ....... done.
Load Package hl7.fhir.pubpack#0.0.3
Installing hl7.fhir.xver-extensions#0.0.1 to the package cache
Fetching:
Installing: done.
Load Package hl7.fhir.xver-extensions#0.0.1
Dependency 'hl7.fhir.us.core' has no id, so can't be referred to in markdown in the IG (00:15.0005)
Installing hl7.fhir.us.core#3.1.0 to the package cache
Fetching:.....
Installing: ..... done.
Initialization complete (00:16.0245)
Load Content (00:16.0246)
Processing Conformance Resources (00:17.0227)
Terminology server: Check for supported code systems for http://snomed.info/sct (00:25.0033)
org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending Http Request: Read timed out
at org.hl7.fhir.r5.utils.client.ClientUtils.sendRequest(ClientUtils.java:332)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:251)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:235)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:226)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueGetResourceRequest(ClientUtils.java:162)
at org.hl7.fhir.r5.utils.client.FHIRToolingClient.getTerminologyCapabilities(FHIRToolingClient.java:185)
at org.hl7.fhir.r5.terminologies.TerminologyClientR5.getTerminologyCapabilities(TerminologyClientR5.java:46)
at org.hl7.fhir.r5.context.BaseWorkerContext.supportsSystem(BaseWorkerContext.java:365)
at org.hl7.fhir.r5.validation.InstanceValidator.checkCode(InstanceValidator.java:920)
at org.hl7.fhir.r5.validation.InstanceValidator.checkCoding(InstanceValidator.java:1488)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:4913)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:4774)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:5024)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:4774)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:5024)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:4774)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:4949)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:4774)
at org.hl7.fhir.r5.validation.InstanceValidator.startInner(InstanceValidator.java:3584)
at org.hl7.fhir.r5.validation.InstanceValidator.start(InstanceValidator.java:3496)
at org.hl7.fhir.r5.validation.InstanceValidator.validateResource(InstanceValidator.java:5456)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:854)
at org.hl7.fhir.r5.validation.InstanceValidator.validate(InstanceValidator.java:830)
at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:4267)
at org.hl7.fhir.igtools.publisher.Publisher.validate(Publisher.java:3369)
at org.hl7.fhir.igtools.publisher.Publisher.loadConformance(Publisher.java:3350)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:804)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:665)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:6945)
Caused by: java.net.SocketTimeoutException: Read timed out
at java.base/java.net.SocketInputStream.socketRead0(Native Method)
at java.base/java.net.SocketInputStream.socketRead(SocketInputStream.java:115)
at java.base/java.net.SocketInputStream.read(SocketInputStream.java:168)
at java.base/java.net.SocketInputStream.read(SocketInputStream.java:140)
at org.apache.http.impl.io.AbstractSessionInputBuffer.fillBuffer(AbstractSessionInputBuffer.java:161)
at org.apache.http.impl.io.SocketInputBuffer.fillBuffer(SocketInputBuffer.java:82)
at org.apache.http.impl.io.AbstractSessionInputBuffer.readLine(AbstractSessionInputBuffer.java:276)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:138)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:56)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:259)
at org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:294)
at org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:257)
at org.apache.http.impl.conn.ManagedClientConnectionImpl.receiveResponseHeader(ManagedClientConnectionImpl.java:207)
at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:273)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:125)
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:679)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:481)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:835)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:108)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:56)
at org.hl7.fhir.r5.utils.client.ClientUtils.sendRequest(ClientUtils.java:330)
... 28 more
Terminology server: Check for supported code systems for http://snomed.info/sct (00:30.0091)
org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending Http Request: Read timed out
at org.hl7.fhir.r5.utils.client.ClientUtils.sendRequest(ClientUtils.java:332)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:251)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:235)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:226)
at org.hl7.fhir.r5.utils.client.ClientUtils.issueGetResourceRequest(ClientUtils.java:162)
at org.hl7.fhir.r5.utils.client.FHIRToolingClient.getTerminologyCapabilities(FHIRToolingClient.java:185)
at org.hl7.fhir.r5.terminologies.TerminologyClientR5.getTerminologyCapabilities(TerminologyClientR5.java:46)
at org.hl7.fhir.r5.context.BaseWorkerContext.supportsSystem(BaseWorkerContext.java:365)
at org.hl7.fhir.r5.validation.InstanceValidator.checkCode(InstanceValidator.java:920)
at org.hl7.fhir.r5.validation.InstanceValidator.checkCoding(InstanceValidator.java:1488)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:4913)
at org.hl7.fhir.r5.validation.InstanceValidator.validateElement(InstanceValidator.java:4774)
at org.hl7.fhir.r5.validation.InstanceValidator.checkChild(InstanceValidator.java:5024)
Mark Kramer (Feb 18 2020 at 00:04):
And now it went through cleanly. Who knows why...
Jose Costa Teixeira (Feb 18 2020 at 05:16):
Life is like a box of chocolates... :)
Jose Costa Teixeira (Feb 18 2020 at 05:17):
(never saw this and cannot replicate, sorry. hope it was a glitch)
Grahame Grieve (Feb 18 2020 at 06:34):
tx.fhir.org was hung - restarted now
Last updated: Apr 12 2022 at 19:14 UTC
