Re: [ferret_users] HDF5 error when loading .nc files

To: Neil Malan <neilcmalan@xxxxxxxxx>

Subject: Re: [ferret_users] HDF5 error when loading .nc files

From: Karl Smith - NOAA Affiliate <karl.smith@xxxxxxxx>

Date: Thu, 24 May 2018 11:35:09 -0700

Arc-authentication-results: i=2; mx.google.com; dkim=pass header.i=@noaa.gov header.s=google header.b=Hla9b2Yw; spf=pass (google.com: domain of karl.smith@xxxxxxxx designates 209.85.220.41 as permitted sender) smtp.mailfrom=karl.smith@xxxxxxxx; dmarc=pass (p=QUARANTINE sp=NONE dis=NONE) header.from=noaa.gov

Arc-authentication-results: i=1; mx.google.com; dkim=pass header.i=@noaa.gov header.s=google header.b=Hla9b2Yw; spf=pass (google.com: domain of karl.smith@xxxxxxxx designates 209.85.220.41 as permitted sender) smtp.mailfrom=karl.smith@xxxxxxxx; dmarc=pass (p=QUARANTINE sp=NONE dis=NONE) header.from=noaa.gov

Arc-message-signature: i=2; a=rsa-sha256; c=relaxed/relaxed; d=google.com; s=arc-20160816; h=list-archive:list-help:list-post:list-id:mailing-list:precedence:cc :to:subject:message-id:date:from:references:in-reply-to:mime-version :arc-authentication-results:arc-message-signature:dkim-signature :arc-authentication-results; bh=OnYGu5VJoOuxWezSq0HzK2EH9QZ1TvBhRVDlxNw4K18=; b=UsWCj4Ir+5gYb1SM9QowMGCKNsLMBaYYHepeDSCZciGRHoG4aY8n9bfjECSK208Y7I hnen9G9uRXwFqQoz/B//B0Uonw0eRafCGlTWB2EdATosoJ358nRHWSWAQzxoMCAd9+Cw znxEaKdbpcIaTa7GEqKcFnM9e6woZiZLyfMMnxCo3ciLQuHbwBYytO3E+W+ixu4UFlAw eVT0t4BjEjeQJIxo+sry5xt6m2w6AyDPrIwf6Iyan1zMrM4FK47JtZs9ha6bBfHaI2gs aGf0zxx1m1FdqH8dJV8OXLyasd7Q8gQOc0ALj/uN5Y11QfD26AudRvK88voC7CZ1znxq w3dg==

Arc-message-signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=google.com; s=arc-20160816; h=cc:to:subject:message-id:date:from:references:in-reply-to :mime-version:dkim-signature:arc-authentication-results; bh=OnYGu5VJoOuxWezSq0HzK2EH9QZ1TvBhRVDlxNw4K18=; b=zNh/OsIc9uLaOlHetQT0cbZvevfEXGiJ/hjwHEcLoSWMNNBIUIByGhvRImyyFjz/Ty /Vn0hm9EsNZZwnbYs9DAiGs9wg72u71bFSw7PhBrZAuExW9lw11wFWMjUKnzch/l6I+J VZYYtLFomDr7reAvG6JMmz7xfUXYezche/Zkm24XZWgYpuTvAe9kqIaWPjbxNpI8Kpb+ Bs4wDcz2vbsRnt10oErpzxifZmJLRRoAVlTNRXggrav6mIliN1mD7xTpiGrqDTC95zOw 3lv4911i2vCABfLSrz8dDEep/dDLObEqy+4t+VYSRJuxTJOU0h1hE6aUHJs4EAKpuhfE rK0Q==

Arc-seal: i=2; a=rsa-sha256; t=1527186911; cv=pass; d=google.com; s=arc-20160816; b=udZyB6b8XM9NQZXsKgBC5OJZf8uiElwYqbn7gbdPQDKCbr8gB2CM5Z8ADHbFHdqE5u m7oqLydMSe/hBHpc6+hZj8apbmZrve94DPSzbD5fXXagm893cEfDOctPpdmhFVXZUQ7Z xxyCNqXSyiX/CF2L3d3qvTi8bkzd7tQOy1lryYu+dIISAVxFjiLQMxMKzl5Cbx/g8qPe r3fwhGb0UprJ3MMmVScQEycY15wz8NdxBhy6mhtR1NLFt5vx3AowM3oz7Es1bm5M8cu5 30VUqFSieILUL+4dSknPWETuc9bxD4JMkQ/v5ZXuAJBQUVhGgmDhrJZHFEAV0cMz1+Ux XC4Q==

Arc-seal: i=1; a=rsa-sha256; t=1527186910; cv=none; d=google.com; s=arc-20160816; b=BkxzH4O9e11zrpdYNy09LTfhwMDEBXL906h1EUE93/D4qE/NbQprSJcnb2f9w69Qfk HTRfxzI1ONFuW4EjtO7HqTKudq+yHWhZ7NU43CA16hgY7Rp54puS5lz/aGJjJdOHzMaJ 6GhJfs/81vTKbfDHw23kl5aMqUSh3E2hqS1NM/abJxk05d/A8icr8uUETmIgIKDM2s11 DPQY5fJ/+LZ1ERv0UwWN9szG2kieuk6qvp31IjnlxuvzqDzKOgWN4qzP16zBCddXLCbg gxvzQO/cs9bZ5dkCozU5M09M9eVjqB52mO74jmZUFLAwlUBQyJF+Pprba8u/68ewq1kn CBGA==

Cc: ferret <ferret_users@xxxxxxxx>

Dkim-signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=noaa.gov; s=google; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :cc:x-original-sender:x-original-authentication-results:precedence :mailing-list:list-id:list-post:list-help:list-archive; bh=OnYGu5VJoOuxWezSq0HzK2EH9QZ1TvBhRVDlxNw4K18=; b=p+Xoc7MZlFsjVod+4Hvs/RLhT3UXDXVgs3IIVtw6WzfLNTf9+hUN+2HyDyvhJuJm2x QWP9SgVUVWWqV4T3P1Ptzq77Rs+WxqRRzbejUyfvbLIk2pJ0bbcPZVxn6G2u5ExKEXH3 PpwDD1nFFBV2PbGCuc1qlN0uUkKZaxdbq2h8kgFR/xsA3oGbwC5cawuPDpxdIzQCS5uS cjZVhxmcxB2jvhl5Q3vPTXoCJ3ynHB8lUShYUic4yef0UYI9O4jY3e1EPx2LEFSvu/TF hZYnLEcbiAJd0mwcLGBiizdWdvdf/A2ieBkPKzQS9oW5U/C6kOATmGI4xUwFdNv+QoEc xlUA==

In-reply-to: <F3B9274A-77ED-4849-ADE8-EBFAAA2F6EB2@gmail.com>

List-archive: <https://groups.google.com/a/noaa.gov/group/ferret_users/>

List-help: <https://support.google.com/a/noaa.gov/bin/topic.py?topic=25838>, <mailto:ferret_users+help@noaa.gov>

List-id: <ferret_users.noaa.gov>

List-post: <https://groups.google.com/a/noaa.gov/group/ferret_users/post>, <mailto:ferret_users@noaa.gov>

Mailing-list: list ferret_users@xxxxxxxx; contact ferret_users+owners@xxxxxxxx

References: <F3B9274A-77ED-4849-ADE8-EBFAAA2F6EB2@gmail.com>

Sender: owner-ferret_users@xxxxxxxx

Hi Neil,

A user (Henry) from Taiwan was also seeing this issue. The HDF5 library is statically linked into the prebuilt Ferret package, if that is what you are using, so changes in the dynamic libraries won't have an affect. Henry was able to build Ferret from the GitHub repository using Homebrew packages built/installed on his system, and that build worked fine for him. So if you are build it yourself and seeing this issue, let me know.

I will be adding a document in the GitHub repository on how to build Ferret on Mac OS X using Homebrew that is similar to that given for PyFerret. (And yes, a Homebrew recipe would be better.) So if you are comfortable using GitHub and Homebrew, this might be the best solution for getting (and updating) Ferret for your system.

Kind regards,

Karl

On Thu, May 24, 2018 at 7:41 AM, Neil Malan <neilcmalan@xxxxxxxxx> wrote:

Hi All

Having just upgraded to Ferret 7.4 (on a Mac, OSX 10.11.6), I now seem unable to use netcdf files in Ferret. I have tried reinstalling both HDF5 and netcdf, and as well as a few different versions of HDF5 (1.10.1 and 1.8.18), and have also reinstalled Ferret. However, I still get the error below:

(I can get to crash using the tutorial, which I suppose is handy in keeping things reproducible!)

NOAA/PMEL TMAP
FERRET v7.4 (optimized)
Darwin 15.6.0 - 04/16/18
24-May-18 16:33

yes?

! To begin we inform FERRET of the "data set" of interest using the
! SET DATA command. The ETOPO60 data set contains the relief of the
! surface of the earth at 120 minute resolution

SET DATA etopo120
**ERROR Ferret crash; signal = 4
HDF5: infinite loop closing library
E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Has anyone else come across this issue?

Kind regards

Neil

--
------------------------------------------
Neil Malan
Postdoctoral Research Fellow
SAEON Egagasini node & Nansen-Tutu Centre,
Department of Oceanography
University of Cape Town

Tel: +27 82 308 7715

Karl M. Smith, Ph.D.
JISAO Univ. Wash. and PMEL NOAA
"The contents of this message are mine personally and do
not necessarily reflect any position of the Government
or the National Oceanic and Atmospheric Administration."