R h2o.init() fails, but h2o server starts from terminal

Question

I am having trouble running h2o from within R. Just installed following R instructions on this page: http://h2o-release.s3.amazonaws.com/h2o/rel-wolpert/2/index.html. Then,

library(h2o)
h2o.init(nthreads = -1, max_mem_size = '2g', ip = "127.0.0.1")

h2o server wouldn't start:

    H2O is not running yet, starting it now...

Note:  In case of errors look at the following log files:
    /var/folders/7y/p9rdbryd5zg5nvtjgdzyshx40000gt/T//RtmpvbbPTR/h2o_arman_started_from_r.out
    /var/folders/7y/p9rdbryd5zg5nvtjgdzyshx40000gt/T//RtmpvbbPTR/h2o_arman_started_from_r.err

java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

Starting H2O JVM and connecting: ............................................................Cannot load library from path lib/osx_64/libxgboost4j_gpu.dylib
Cannot load library from path lib/libxgboost4j_gpu.dylib
Failed to load library from both native path and jar!
Cannot load library from path lib/osx_64/libxgboost4j_omp.dylib
Cannot load library from path lib/libxgboost4j_omp.dylib
Failed to load library from both native path and jar!
Found XGBoost backend with library: xgboost4j_minimal
Your system supports only minimal version of XGBoost (no GPUs, no multithreading)!
----- H2O started  -----
Build git branch: master
Build git hash: a0f976c49acfa9750b7887b1cda6408d298913f4
Build git describe: jenkins-master-4214
Build project version: 3.19.0.4215 (latest version: 3.18.0.2)
Build age: 16 hours and 15 minutes
Built by: 'jenkins'
Built on: '2018-02-26 07:35:56'
Watchdog Build git branch: (unknown)
Watchdog Build git hash: (unknown)
Watchdog Build git describe: (unknown)
Watchdog Build project version: (unknown)
Watchdog Built by: (unknown)
Watchdog Built on: (unknown)
XGBoost Build git branch: (unknown)
XGBoost Build git hash: (unknown)
XGBoost Build git describe: (unknown)
XGBoost Build project version: (unknown)
XGBoost Built by: (unknown)
XGBoost Built on: (unknown)
KrbStandalone Build git branch: (unknown)
KrbStandalone Build git hash: (unknown)
KrbStandalone Build git describe: (unknown)
KrbStandalone Build project version: (unknown)
KrbStandalone Built by: (unknown)
KrbStandalone Built on: (unknown)
Processed H2O arguments: [-name, H2O_started_from_R_arman_nbd116, -ip, 127.0.0.1, -port, 2341, -ice_root, /var/folders/7y/p9rdbryd5zg5nvtjgdzyshx40000gt/T//RtmpvbbPTR]
Java availableProcessors: 8
Java heap totalMemory: 245.5 MB
Java heap maxMemory: 1.78 GB
Java version: Java 1.8.0_111 (from Oracle Corporation)
JVM launch parameters: [-Xmx2g, -ea]
OS version: Mac OS X 10.13.1 (x86_64)
Machine physical memory: 16.00 GB
X-h2o-cluster-id: 1519649491546
User name: 'arman'
IPv6 stack selected: false
Network address/interface is not reachable in 150ms: /fe80:0:0:0:75d0:fa45:58ee:6f07%utun0/name:utun0 (utun0)
Network address/interface is not reachable in 150ms: /fe80:0:0:0:5448:2bff:fec7:2829%awdl0/name:awdl0 (awdl0)
Network address/interface is not reachable in 150ms: /fe80:0:0:0:1846:22ba:65a6:e16b%en0/name:en0 (en0)
Network address/interface is not reachable in 150ms: /192.168.0.9/name:en0 (en0)
Network address/interface is not reachable in 150ms: /fe80:0:0:0:0:0:0:1%lo0/name:lo0 (lo0)
Network address/interface is not reachable in 150ms: /0:0:0:0:0:0:0:1/name:lo0 (lo0)
Network address/interface is not reachable in 150ms: /127.0.0.1/name:lo0 (lo0)
IP address not found on this machine 
[1] "127.0.0.1"
[1] 2341
[1] TRUE
[1] -1
[1] "Failed to connect to 127.0.0.1 port 2341: Connection refused"
[1] 0
Error in h2o.init(nthreads = -1, max_mem_size = "2g", ip = "127.0.0.1",  : 
  H2O failed to start, stopping execution.

On the other hand, I can run the server from the terminal

java -jar /Users/arman/Library/R/3.4/library/h2o/java/h2o.jar
# Retrieved the location of jar file in R using  h2o:::.h2o.downloadJar()

The above command works. I can continue running from terminal, but h2o.init provides many convenience options as well as code consistency.

Any ideas why h2o fails to initialize from R? Also, tried from Python and had the same problem.

OS: Mac OS X ver 10.13.1

java version "1.8.0_111" Java(TM) SE Runtime Environment (build 1.8.0_111-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

h2o version: 3.19.0.4215

R version: 3.4.3

Darren Cook Darren Cook · Accepted Answer · 2018-02-28T09:24:17

The very strange thing in your example is you do not mention port in your h2o.init() and yet it has tried to start on port 2341.

Either:

you specified port, and didn't show it in your question
You have the environmental variable H2O_R_CMD_CHECK_DOC_EXAMPLES_PORT set.

Do try using the default port (54321).

Generally, when H2O won't start on a certain port it is because either something is already running there, or because of a firewall issue. Given that it works from the commandline, my guess is that the R application needs to be given permission to access localhost on your chosen port. (On Windows it has a dialog popup the first time you try to use it; is Mac doing something similar?)

R h2o.init() fails, but h2o server starts from terminal

2 Answers