py4j.protocol.Py4JNetworkError: Answer from Java side is empty: hail, download files

Hail Query & hailctl
1

Hello, I have installed hail using pycharm not from github nor conda. I was trying read 1k genome vcf data:
hl.import_vcf(‘data/1kg.vcf.bgz’).write(‘data/1kg.mt’, overwrite=True)
mt = hl.read_matrix_table(‘data/1kg.mt’)
The error:

/shire/zillur/learning/python/project1/venv/bin/python /shire/zillur/learning/python/project1/gwas_hail_1.py
19/09/03 11:58:06 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform… using builtin-java classes where applicable
Using Spark’s default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to “WARN”.
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Running on Apache Spark version 2.4.1
SparkUI available at http://dutillab:4040
Welcome to
__ __ <>__
/ /_/ /__ __/ /
/ __ / _ / / / /_/ /_/\_,_/_/_/ version 0.2.20-dd6c996e7db5 LOGGING: writing to /shire/zillur/learning/python/project1/hail-20190903-1158-0.2.20-dd6c996e7db5.log 2019-09-03 11:58:18 Hail: INFO: downloading 1KG VCF ... Source: https://storage.googleapis.com/hail-tutorial/1kg.vcf.bgz 2019-09-03 11:58:19 Hail: INFO: importing VCF and writing to matrix table... ERROR: dlopen("/tmp/libhail7063416592875974503.so"): /lib64/libstdc++.so.6: version CXXABI_1.3.8’ not found (required by /tmp/libhail7063416592875974503.so)
FATAL: caught exception java.lang.UnsatisfiedLinkError: /tmp/libhail7063416592875974503.so: /lib64/libstdc++.so.6: version CXXABI_1.3.8' not found (required by /tmp/libhail7063416592875974503.so) java.lang.UnsatisfiedLinkError: /tmp/libhail7063416592875974503.so: /lib64/libstdc++.so.6: version CXXABI_1.3.8’ not found (required by /tmp/libhail7063416592875974503.so)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
at java.lang.Runtime.load0(Runtime.java:809)
at java.lang.System.load(System.java:1086)
at is.hail.nativecode.NativeCode.(NativeCode.java:30)
at is.hail.nativecode.NativeBase.(NativeBase.scala:20)
at is.hail.annotations.Region.(Region.scala:180)
at is.hail.annotations.Region$.apply(Region.scala:16)
at is.hail.annotations.Region$.scoped(Region.scala:18)
at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:7)
at is.hail.backend.Backend.execute(Backend.scala:86)
at is.hail.backend.Backend.executeJSON(Backend.scala:92)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1159, in send_command
raise Py4JNetworkError(“Answer from Java side is empty”)
py4j.protocol.Py4JNetworkError: Answer from Java side is empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 985, in send_command
response = connection.send_command(command)
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1164, in send_command
“Error while receiving”, e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/gwas_hail_1.py”, line 8, in
hl.utils.get_1kg(‘data/’)
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/hail/utils/tutorial.py”, line 73, in get_1kg
hl.import_vcf(cluster_readable_vcf, min_partitions=16).write(matrix_table_path, overwrite=True)
File “</shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/decorator.py:decorator-gen-1018>”, line 2, in write
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/hail/typecheck/check.py”, line 585, in wrapper
return original_func(*args, **kwargs)
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/hail/matrixtable.py”, line 2508, in write
Env.backend().execute(MatrixWrite(self._mir, writer))
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/hail/backend/backend.py”, line 108, in execute
result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1257, in call
answer, self.gateway_client, self.target_id, self.name)
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/hail/utils/java.py”, line 213, in deco
return f(*args, **kwargs)
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/protocol.py”, line 336, in get_return_value
format(target_id, “.”, name))
py4j.protocol.Py4JError: An error occurred while calling o50.executeJSON
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:40268)
Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/shire/zillur/learning/python/project1/venv/lib64/python3.6/site-packages/py4j/java_gateway.py”, line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused

Process finished with exit code 1

2

Based on error, my guess is that your version of the C++ standard library is incompatible with the version of Hail you have. Your system must have at least GCC 4.9 installed in order to have access to CXXABI_1.3.8. What is the output of gcc --version ?

3

Thank you John.
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36). How can I get newer version of gcc? Best, Zillur

4

Probably by running something like: sudo yum install gcc-c++ ?

5

@zillurbmb51, Even if you get a recent version of gcc installed, you will need a newer version of RHEL. RHEL 4.8.5 was released in December 2004 and uses a version of the GNU C Standard Library with which Hail is incompatible. RHEL 7 should be sufficient for use with Hail.

6

Hello, Thank you. Now I have gcc 7 in centos 7
`gcc (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5 )
I have reinstalled hail as follows:
conda create -n hail python==3.6
conda activate hail
sudo pip3 install hail
sudo python3.6 -m pip install -U --force-reinstall hail
Now I am getting following error: Any help?

(hail) [zillur@dutillab hail]$ python3.6 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
Initializing Spark and Hail with default parameters...
19/09/09 10:22:08 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Running on Apache Spark version 2.4.1
SparkUI available at http://dutillab:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.21-f16fd64e0d77
LOGGING: writing to /shire/zillur/hail/hail-20190909-1022-0.2.21-f16fd64e0d77.log
2019-09-09 10:22:20 Hail: INFO: balding_nichols_model: generating genotypes for 3 populations, 100 samples, and 100 variants...
ERROR: dlopen("/tmp/libhail1432194653321224887.so"): /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /tmp/libhail1432194653321224887.so)
FATAL: caught exception java.lang.UnsatisfiedLinkError: /tmp/libhail1432194653321224887.so: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /tmp/libhail1432194653321224887.so)
java.lang.UnsatisfiedLinkError: /tmp/libhail1432194653321224887.so: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /tmp/libhail1432194653321224887.so)
	at java.lang.ClassLoader$NativeLibrary.load(Native Method)
	at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
	at java.lang.Runtime.load0(Runtime.java:809)
	at java.lang.System.load(System.java:1086)
	at is.hail.nativecode.NativeCode.<clinit>(NativeCode.java:30)
	at is.hail.nativecode.NativeBase.<init>(NativeBase.scala:20)
	at is.hail.annotations.Region.<init>(Region.scala:180)
	at is.hail.annotations.Region$.apply(Region.scala:16)
	at is.hail.annotations.Region$.scoped(Region.scala:18)
	at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:7)
	at is.hail.backend.Backend.execute(Backend.scala:86)
	at is.hail.backend.Backend.executeJSON(Backend.scala:92)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.lang.Thread.run(Thread.java:748)
ERROR:root:Exception while sending command.
Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1159, in send_command
    raise Py4JNetworkError("Answer from Java side is empty")
py4j.protocol.Py4JNetworkError: Answer from Java side is empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 985, in send_command
    response = connection.send_command(command)
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1164, in send_command
    "Error while receiving", e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/hail/matrixtable.py", line 2389, in _force_count_rows
    return Env.backend().execute(MatrixToValueApply(self._mir, {'name': 'ForceCountMatrixTable'}))
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/hail/backend/backend.py", line 108, in execute
    result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1257, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/hail/utils/java.py", line 213, in deco
    return f(*args, **kwargs)
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/protocol.py", line 336, in get_return_value
    format(target_id, ".", name))
py4j.protocol.Py4JError: An error occurred while calling o50.executeJSON
ERROR:root:Exception while sending command.
Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1159, in send_command
    raise Py4JNetworkError("Answer from Java side is empty")
py4j.protocol.Py4JNetworkError: Answer from Java side is empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 985, in send_command
    response = connection.send_command(command)
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1164, in send_command
    "Error while receiving", e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:39100)
Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 929, in _get_connection
    connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1067, in start
    self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:39100)
Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 929, in _get_connection
    connection = self.deque.pop()
IndexError: pop from an empty deque

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/shire/anaconda2/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1067, in start
    self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
7

what platform are you running on? You’ll probably need to compile hail yourself: https://hail.is/docs/0.2/getting_started_developing.html#building-hail

8

Thank you. I have tried from the link you shared. Getting this:
(hail) [zillur@dutillab hail]$ git clone https://github.com/hail-is/hail.git

Cloning into 'hail'...
    remote: Enumerating objects: 43, done.
    remote: Counting objects: 100% (43/43), done.
    remote: Compressing objects: 100% (42/42), done.
    remote: Total 91935 (delta 14), reused 3 (delta 1), pack-reused 91892
    Receiving objects: 100% (91935/91935), 71.62 MiB | 22.92 MiB/s, done.
    Resolving deltas: 100% (55407/55407), done.
    (hail) [zillur@dutillab hail]$ cd hail/hail/
    (hail) [zillur@dutillab hail]$ ls
    benchmark       diagnose.sh            env_var.mk           gradlew.bat               pgradle   scripts          test-jar-with-dependencies.xml  www
    build.gradle    Dockerfile.hail-build  get-deployed-sha.sh  install-gcs-connector.sh  prebuilt  settings.gradle  testng-cpp-codegen.xml
    build.sbt       Dockerfile.hail-run    gradle               list_pypi_versions.py     project   src              testng-distributed-backend.xml
    code_style.xml  Dockerfile.hailtop     gradlew              Makefile                  python    style-guide.md   testng.xml
    (hail) [zillur@dutillab hail]$ make install-wheel HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1
    make: *** No rule to make target 'install-wheel'.  Stop.
    (hail) [zillur@dutillab hail]$ ls ../
    apiserver  batch2        datasets      gateway           image-fetcher  monitoring  project    router-resolver  setup.cfg        vdc
    auth       build.yaml    docker        gateway-internal  letsencrypt    notebook    pylintrc   scheduler        site
    AUTHORS    ci            env-setup.sh  generate-uid.sh   LICENSE        notebook2   README.md  scorecard        ukbb-rg
    batch      cloud-sql.mk  etc           hail              Makefile       pipeline    router     SECRETS.md       until-with-fuel
    (hail) [zillur@dutillab hail]$ cd ../
    (hail) [zillur@dutillab hail]$ make install-wheel HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1
    make: *** No rule to make target 'install-wheel'.  Stop.
9

ack that’s out of date. Should be install not install-wheel

10

Thank you. Still doesn’t work.
(hail) [zillur@dutillab hail]$ sudo make install HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1
[sudo] password for zillur:
SPARK_VERSION is set to “2.4.1” which is different from old value “2.4.0”
printf “2.4.1” > env/SPARK_VERSION
echo ‘[Build Metadata]’ > src/main/resources/build-info.properties
echo ‘user=root’ >> src/main/resources/build-info.properties
echo ‘revision=b42ffc0c9feb43cca19a3a743a535e7d93cfb93d’ >> src/main/resources/build-info.properties
echo ‘branch=master’ >> src/main/resources/build-info.properties
echo ‘date=2019-09-09T15:10:01Z’ >> src/main/resources/build-info.properties
echo ‘url=https://github.com/hail-is/hail.git’ >> src/main/resources/build-info.properties
echo ‘sparkVersion=2.4.1’ >> src/main/resources/build-info.properties
echo ‘hailPipVersion=0.2.21’ >> src/main/resources/build-info.properties
make -C src/main/c prebuilt
make[1]: Entering directory ‘/shire/zillur/hail/hail/hail/src/main/c’
make[1]: *** No rule to make target ‘lz4.h’, needed by ‘build/Decoder.o’. Stop.
make[1]: Leaving directory ‘/shire/zillur/hail/hail/hail/src/main/c’
make: *** [Makefile:350: native-lib-prebuilt] Error 2

11

You need to install lz4. Anyway, it appears that you don’t have a recent version of libstdc++. What version of g++ do you have installed?

12

Thank you. The g++ version is:
g++ (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5)
And the lz4:
(hail) [zillur@dutillab hail]$ sudo yum install lz4
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
* base: mirror.linux.duke.edu
* centos-sclo-rh: mirror.fileplanet.com
* centos-sclo-sclo: mirror.teklinks.com
* elrepo: mirror.pit.teraswitch.com
* epel: mirror.siena.edu
* extras: mirror.mojohost.com
* updates: mirrors.gigenet.com
Package lz4-1.7.5-2.el7.x86_64 already installed and latest version
Nothing to do

13

You need the development version of lz4, in apt-get this is called liblz4-dev, you’ll need to find the equivalent package for yum. Also, after updating, you’ll need to run make clean before trying to build again.

It seems likely that your worker nodes do not have g++ 7.3.1. Every node in the Spark cluster will need the same version of g++.

14

Thank you. Now I have the lz4-devel, gcc 9.2 for all nodes and getting this:
(base) [zillur@dutillab hail]$ sudo make clean
rm -rf env
make -C www clean
make[1]: Entering directory /shire/zillur/hail/hail/hail/www' rm -f 404.html references.html index.html make[1]: Leaving directory/shire/zillur/hail/hail/hail/www’
make -C src/main/c clean
make[1]: Entering directory /shire/zillur/hail/hail/hail/src/main/c' g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Upcalls.cpp -MG -M -MF build/Upcalls.d -MT build/Upcalls.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux testutils/unit-tests.cpp -MG -M -MF build/testutils/unit-tests.d -MT build/testutils/unit-tests.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux test.cpp -MG -M -MF build/test.d -MT build/test.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Region_test.cpp -MG -M -MF build/Region_test.d -MT build/Region_test.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Region.cpp -MG -M -MF build/Region.d -MT build/Region.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux PartitionIterators.cpp -MG -M -MF build/PartitionIterators.d -MT build/PartitionIterators.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ObjectArray.cpp -MG -M -MF build/ObjectArray.d -MT build/ObjectArray.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeStatus.cpp -MG -M -MF build/NativeStatus.d -MT build/NativeStatus.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativePtr.cpp -MG -M -MF build/NativePtr.d -MT build/NativePtr.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeModule.cpp -MG -M -MF build/NativeModule.d -MT build/NativeModule.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeLongFunc.cpp -MG -M -MF build/NativeLongFunc.d -MT build/NativeLongFunc.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeCodeSuite.cpp -MG -M -MF build/NativeCodeSuite.d -MT build/NativeCodeSuite.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeBoot.cpp -MG -M -MF build/NativeBoot.d -MT build/NativeBoot.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Logging.cpp -MG -M -MF build/Logging.d -MT build/Logging.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ibs.cpp -MG -M -MF build/ibs.d -MT build/ibs.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux FS.cpp -MG -M -MF build/FS.d -MT build/FS.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Encoder.cpp -MG -M -MF build/Encoder.d -MT build/Encoder.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Decoder.cpp -MG -M -MF build/Decoder.d -MT build/Decoder.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux davies.cpp -MG -M -MF build/davies.d -MT build/davies.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux cache-tests.cpp -MG -M -MF build/cache-tests.d -MT build/cache-tests.o g++: error: unrecognized command line option ‘-std=c++14’ g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ApproximateQuantiles_test.cpp -MG -M -MF build/ApproximateQuantiles_test.d -MT build/ApproximateQuantiles_test.o g++: error: unrecognized command line option ‘-std=c++14’ rm -rf build libsimdpp-2.1 lib make[1]: Leaving directory/shire/zillur/hail/hail/hail/src/main/c’
./gradlew clean -Dspark.version=2.4.0 -Dpy4j.version

BUILD SUCCESSFUL in 0s
1 actionable task: 1 up-to-date
rm -rf build/
rm -rf python/hail/hail-all-spark.jar
rm -rf python/README.md
(base) [zillur@dutillab hail]$ sudo make install HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1
SHORT_REVISION is set to "b42ffc0c9feb" which is different from old value ""
printf "b42ffc0c9feb" > env/SHORT_REVISION
HAIL_PIP_VERSION is set to "0.2.21" which is different from old value ""
printf "0.2.21" > env/HAIL_PIP_VERSION
echo 0.2.21-b42ffc0c9feb > python/hail/hail_version
echo 0.2.21 > python/hail/hail_pip_version
cp -f python/hail/hail_version python/hailtop/hailctl/hail_version
REVISION is set to "b42ffc0c9feb43cca19a3a743a535e7d93cfb93d" which is different from old value ""
printf "b42ffc0c9feb43cca19a3a743a535e7d93cfb93d" > env/REVISION
BRANCH is set to "master" which is different from old value ""
printf "master" > env/BRANCH
URL is set to "https://github.com/hail-is/hail.git" which is different from old value ""
printf "https://github.com/hail-is/hail.git" > env/URL
SPARK_VERSION is set to "2.4.1" which is different from old value ""
printf "2.4.1" > env/SPARK_VERSION
echo '[Build Metadata]' > src/main/resources/build-info.properties
echo 'user=zillur' >> src/main/resources/build-info.properties
echo 'revision=b42ffc0c9feb43cca19a3a743a535e7d93cfb93d' >> src/main/resources/build-info.properties
echo 'branch=master' >> src/main/resources/build-info.properties
echo 'date=2019-09-09T16:45:30Z' >> src/main/resources/build-info.properties
echo 'url=https://github.com/hail-is/hail.git' >> src/main/resources/build-info.properties
echo 'sparkVersion=2.4.1' >> src/main/resources/build-info.properties
echo 'hailPipVersion=0.2.21' >> src/main/resources/build-info.properties
make -C src/main/c prebuilt
make[1]: Entering directory `/shire/zillur/hail/hail/hail/src/main/c'
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Upcalls.cpp -MG -M -MF build/Upcalls.d -MT build/Upcalls.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux testutils/unit-tests.cpp -MG -M -MF build/testutils/unit-tests.d -MT build/testutils/unit-tests.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux test.cpp -MG -M -MF build/test.d -MT build/test.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Region_test.cpp -MG -M -MF build/Region_test.d -MT build/Region_test.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Region.cpp -MG -M -MF build/Region.d -MT build/Region.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux PartitionIterators.cpp -MG -M -MF build/PartitionIterators.d -MT build/PartitionIterators.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ObjectArray.cpp -MG -M -MF build/ObjectArray.d -MT build/ObjectArray.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeStatus.cpp -MG -M -MF build/NativeStatus.d -MT build/NativeStatus.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativePtr.cpp -MG -M -MF build/NativePtr.d -MT build/NativePtr.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeModule.cpp -MG -M -MF build/NativeModule.d -MT build/NativeModule.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeLongFunc.cpp -MG -M -MF build/NativeLongFunc.d -MT build/NativeLongFunc.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeCodeSuite.cpp -MG -M -MF build/NativeCodeSuite.d -MT build/NativeCodeSuite.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux NativeBoot.cpp -MG -M -MF build/NativeBoot.d -MT build/NativeBoot.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Logging.cpp -MG -M -MF build/Logging.d -MT build/Logging.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ibs.cpp -MG -M -MF build/ibs.d -MT build/ibs.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux FS.cpp -MG -M -MF build/FS.d -MT build/FS.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Encoder.cpp -MG -M -MF build/Encoder.d -MT build/Encoder.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Decoder.cpp -MG -M -MF build/Decoder.d -MT build/Decoder.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux davies.cpp -MG -M -MF build/davies.d -MT build/davies.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux cache-tests.cpp -MG -M -MF build/cache-tests.d -MT build/cache-tests.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux ApproximateQuantiles_test.cpp -MG -M -MF build/ApproximateQuantiles_test.d -MT build/ApproximateQuantiles_test.o
g++: error: unrecognized command line option ‘-std=c++14’
g++ -o build/NativeBoot.o -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux -MD -MF build/NativeBoot.d -MT build/NativeBoot.o -c NativeBoot.cpp
g++: error: unrecognized command line option ‘-std=c++14’
make[1]: *** [build/NativeBoot.o] Error 1
make[1]: Leaving directory `/shire/zillur/hail/hail/hail/src/main/c'
make: *** [native-lib-prebuilt] Error 2
15

When I try to download the ikg vcf file, I am getting:
>>> hl.init()
19/09/09 12:49:34 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform… using builtin-java classes where applicable
Using Spark’s default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to “WARN”.
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Running on Apache Spark version 2.4.1
SparkUI available at http://dutillab:4040
Welcome to
__ __ <>__
/ /_/ /__ __/ /
/ __ / _ / / / /_/ /_/\_,_/_/_/ version 0.2.21-f16fd64e0d77 LOGGING: writing to /shire/zillur/hail/hail-20190909-1249-0.2.21-f16fd64e0d77.log >>> from hail.plot import show >>> from pprint import pprint >>> hl.plot.output_notebook() In : In : hl.utils.get_1kg('data/') Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'hl' is not defined In : In : In : hl.utils.get_1kg('data/') Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'hl' is not defined In : In : In : hl.utils.get_1kg('data/') Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'hl' is not defined In : In : import hail as hl In : from hail.plot import show In : from pprint import pprint In : hl.utils.get_1kg('data/') 2019-09-09 12:51:12 Hail: INFO: downloading 1KG VCF ... Source: https://storage.googleapis.com/hail-tutorial/1kg.vcf.bgz 2019-09-09 12:51:13 Hail: INFO: importing VCF and writing to matrix table... ERROR: dlopen("/tmp/libhail2217219008725920630.so"): /lib64/libstdc++.so.6: versionCXXABI_1.3.8’ not found (required by /tmp/libhail2217219008725920630.so)
FATAL: caught exception java.lang.UnsatisfiedLinkError: /tmp/libhail2217219008725920630.so: /lib64/libstdc++.so.6: version CXXABI_1.3.8' not found (required by /tmp/libhail2217219008725920630.so) java.lang.UnsatisfiedLinkError: /tmp/libhail2217219008725920630.so: /lib64/libstdc++.so.6: versionCXXABI_1.3.8’ not found (required by /tmp/libhail2217219008725920630.so)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
at java.lang.Runtime.load0(Runtime.java:809)
at java.lang.System.load(System.java:1086)
at is.hail.nativecode.NativeCode.(NativeCode.java:30)
at is.hail.nativecode.NativeBase.(NativeBase.scala:20)
at is.hail.annotations.Region.(Region.scala:180)
at is.hail.annotations.Region$.apply(Region.scala:16)
at is.hail.annotations.Region$.scoped(Region.scala:18)
at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:7)
at is.hail.backend.Backend.execute(Backend.scala:86)
at is.hail.backend.Backend.executeJSON(Backend.scala:92)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File “/usr/lib/python3.6/site-packages/py4j/java_gateway.py”, line 1159, in send_command
raise Py4JNetworkError(“Answer from Java side is empty”)
py4j.protocol.Py4JNetworkError: Answer from Java side is empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/py4j/java_gateway.py", line 985, in send_command
    response = connection.send_command(command)
  File "/usr/lib/python3.6/site-packages/py4j/java_gateway.py", line 1164, in send_command
    "Error while receiving", e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.6/site-packages/hail/utils/tutorial.py", line 73, in get_1kg
    hl.import_vcf(cluster_readable_vcf, min_partitions=16).write(matrix_table_path, overwrite=True)
  File "</usr/lib/python3.6/site-packages/decorator.py:decorator-gen-1020>", line 2, in write
  File "/usr/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
    return __original_func(*args_, **kwargs_)
  File "/usr/lib/python3.6/site-packages/hail/matrixtable.py", line 2508, in write
    Env.backend().execute(MatrixWrite(self._mir, writer))
  File "/usr/lib/python3.6/site-packages/hail/backend/backend.py", line 108, in execute
    result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
  File "/usr/lib/python3.6/site-packages/py4j/java_gateway.py", line 1257, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/usr/lib/python3.6/site-packages/hail/utils/java.py", line 213, in deco
    return f(*args, **kwargs)
  File "/usr/lib/python3.6/site-packages/py4j/protocol.py", line 336, in get_return_value
    format(target_id, ".", name))
py4j.protocol.PyIn : 
4JError: An error occurred while calling o50.executeJSON
16

A few things:

  1. You should probably not run sudo make install, that gives too much privilege to our build system. If the user compiling hail is also running hail, make install is sufficient (it will use pip’s local install method). If you need to install hail for all users on the system, I recommend make wheel && sudo make install
  2. What is the output of g++ --version? Hail’s error output is very clear: the g++ you are using to build does not support c++14. This support was completed in GCC 5.0, so the g++ below must not be version 5.0
g++ -march=corei7-avx -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.el7_6.x86_64/include/linux Upcalls.cpp -MG -M -MF build/Upcalls.d -MT build/Upcalls.o
g++: error: unrecognized command line option ‘-std=c++14’
  1. The second message indicates that the standard library installed at /lib64/libstdc++.so.6 uses an ABI before version 1.3.8. The following command will tell you what ABI versions are supported. That command needs to print CXXABI_1.3.8 or hail will be unable to run correctly.
strings /usr/lib/libstdc++.so.6 | grep CXXABI
  1. What is your compute environment? Do you have a Spark cluster?
17

Thank you.
export LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
Solved the issue. Now I can run the GWAS tutorial. How can I check my compute environment and Spark? Also is there any guideline to explore my own vcf file? In the GWAS tutorial a sample phonetype (Caffeine consumption) was analyzed. How can I find other phenotypes from my vcf files. Best, Zillur

18

Have you installed Spark on several computers and connected those computers together? If no, then you don’t have a Spark cluster. In that case, you’re using hail in “local mode”, i.e. you’re using all the CPU cores on one machine.

VCF files do not contain phenotype information. Whoever gave you those VCF files must have phenotype information stored separately.

19

A post was split to a new topic: While running a GWAS / linear regression I get: “Answer from Java side empty” and “undefined symbol: cblas_dgemv”