Comments (18)
rimmartin
commented on July 22, 2024
http://hdf-ni.github.io/hdf5.node/doc/install-setup.html
Give
npm install hdf5 --fallback-to-build –hdf5_home_mac=/usr/local/hdf5
a try. If it still fails we'll investigate further
from hdf5.node.
rimmartin
commented on July 22, 2024
Clean up by getting rid of the build folder and it's linux project placed there by node-pre-gyp
from hdf5.node.
rimmartin
commented on July 22, 2024
It should be looking for a
libhdf5.dylib instead of libhdf5.so.100
from hdf5.node.
duckontheweb
commented on July 22, 2024
npm install hdf5 --fallback-to-build --hdf5_home_mac=/usr/local/hdf5 installs without error, but I now get a different error on require:
> var h = require("hdf5")
Error: Cannot find module './build/Release/hdf5'
at Function.Module._resolveFilename (module.js:325:15)
at Function.Module._load (module.js:276:25)
at Module.require (module.js:353:17)
at require (internal/module.js:12:17)
at Object.<anonymous> (/opt/hdf5-test/node_modules/hdf5/index.js:4:25)
at Module._compile (module.js:409:26)
at Object.Module._extensions..js (module.js:416:10)
at Module.load (module.js:343:32)
at Function.Module._load (module.js:300:12)
at Module.require (module.js:353:17)
from hdf5.node.
rimmartin
commented on July 22, 2024
I can't repeat this on my linux box but after work today I'll have access to a mac and will investigate then
from hdf5.node.
rimmartin
commented on July 22, 2024
to get to the hdf5 module you will need
var h = require("hdf5").hdf5;
but I don't expect that to fix this. This project has modules for different parts like
var h5im = require("hdf5").h5im;
get the image interface
from hdf5.node.
duckontheweb
commented on July 22, 2024
Okay, thanks. I'm running this on Linux as well (Debian), so I'm not sure
if experimenting on a Mac will help or not. I'll try to troubleshoot the
latest error a bit more and let you know if I find anything.
…On Fri, Dec 9, 2016 at 11:38 AM, rimmartin ***@***.***> wrote:
to get to the hdf5 module you will need
var h = require("hdf5").hdf5;
but I don't expect that to fix this. This project has modules for
different parts like
var h5im = require("hdf5").h5im;
get the image interface
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#34 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AGjzeZ4pzEuqtWL2sLYMt3xVt8wgPuleks5rGaASgaJpZM4LIbqg>
.
from hdf5.node.
duckontheweb
commented on July 22, 2024
I just wiped out my build and started over using npm install hdf5 --fallback-to-build --hdf5_home_mac=/usr/local/hdf5 and the build is now failing with the following error:
In file included from ../src/hdf5.cc:2:0:
../src/file.h:11:18: fatal error: hdf5.h: No such file or directory
#include "hdf5.h"
^
compilation terminated.
hdf5.target.mk:104: recipe for target 'Release/obj.target/hdf5/src/hdf5.o' failed
This is what I was getting when I was using the wrong path to my HDF5 install, so I'm guessing that the --hdf5_home_mac just isn't picking up the library.
from hdf5.node.
duckontheweb
commented on July 22, 2024
In case it's helpful, here's the full output for a successful install. This is the one that yields the original error.
root@44089d5f6762:/opt/test-project# npm install hdf5 --fallback-to-build --hdf5_home_linux=/usr/local/hdf5
npm info it worked if it ends with ok
npm info using [email protected]
npm info using [email protected]
npm WARN package.json [email protected] No description
npm WARN package.json [email protected] No repository field.
npm WARN package.json [email protected] No README data
npm info addNameTag [ 'hdf5', 'latest' ]
npm info attempt registry request try #1 at 12:34:52 AM
npm http request GET https://registry.npmjs.org/hdf5
npm http 304 https://registry.npmjs.org/hdf5
npm info install [email protected] into /opt/test-project
npm info installOne [email protected]
npm info preinstall [email protected]
npm info package.json [email protected] license should be a valid SPDX license expression
npm info build /opt/test-project/node_modules/hdf5
npm info linkStuff [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/mkdirp
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/nopt
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/npmlog
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/rc
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/request
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/rimraf
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/semver
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/tar
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info build /opt/test-project/node_modules/hdf5/node_modules/node-pre-gyp/node_modules/tar-pack
npm info preinstall [email protected]
npm info linkStuff [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info install [email protected]
npm info postinstall [email protected]
npm info install [email protected]
> [email protected] install /opt/test-project/node_modules/hdf5
> node-pre-gyp install --fallback-to-build
node-pre-gyp info it worked if it ends with ok
node-pre-gyp info using [email protected]
node-pre-gyp info using [email protected] | linux | x64
node-pre-gyp info check checked for "/opt/test-project/node_modules/hdf5/lib/binding/hdf5.node" (not found)
node-pre-gyp http GET https://hdf5.node.s3-us-west-2.amazonaws.com/v0.2.1/hdf5-v0.2.1-node-v46-linux-x64.tar.gz
node-pre-gyp http Hostname/IP doesn't match certificate's altnames: "Host: hdf5.node.s3-us-west-2.amazonaws.com. is not in the cert's altnames: DNS:s3-us-west-2.amazonaws.com, DNS:*.s3-us-west-2.amazonaws.com, DNS:s3.us-west-2.amazonaws.com, DNS:*.s3.us-west-2.amazonaws.com, DNS:s3.dualstack.us-west-2.amazonaws.com, DNS:*.s3.dualstack.us-west-2.amazonaws.com, DNS:*.s3.amazonaws.com" (falling back to source compile with node-gyp)
gyp info it worked if it ends with ok
gyp info using [email protected]
gyp info using [email protected] | linux | x64
gyp info ok
gyp info it worked if it ends with ok
gyp info using [email protected]
gyp info using [email protected] | linux | x64
gyp info spawn /usr/bin/python2
gyp info spawn args [ '/usr/local/lib/node_modules/npm/node_modules/node-gyp/gyp/gyp_main.py',
gyp info spawn args 'binding.gyp',
gyp info spawn args '-f',
gyp info spawn args 'make',
gyp info spawn args '-I',
gyp info spawn args '/opt/test-project/node_modules/hdf5/build/config.gypi',
gyp info spawn args '-I',
gyp info spawn args '/usr/local/lib/node_modules/npm/node_modules/node-gyp/addon.gypi',
gyp info spawn args '-I',
gyp info spawn args '/root/.node-gyp/4.7.0/include/node/common.gypi',
gyp info spawn args '-Dlibrary=shared_library',
gyp info spawn args '-Dvisibility=default',
gyp info spawn args '-Dnode_root_dir=/root/.node-gyp/4.7.0',
gyp info spawn args '-Dnode_gyp_dir=/usr/local/lib/node_modules/npm/node_modules/node-gyp',
gyp info spawn args '-Dnode_lib_file=node.lib',
gyp info spawn args '-Dmodule_root_dir=/opt/test-project/node_modules/hdf5',
gyp info spawn args '--depth=.',
gyp info spawn args '--no-parallel',
gyp info spawn args '--generator-output',
gyp info spawn args 'build',
gyp info spawn args '-Goutput_dir=.' ]
gyp info ok
gyp info it worked if it ends with ok
gyp info using [email protected]
gyp info using [email protected] | linux | x64
gyp info spawn make
gyp info spawn args [ 'BUILDTYPE=Release', '-C', 'build' ]
make: Entering directory '/opt/test-project/node_modules/hdf5/build'
CXX(target) Release/obj.target/hdf5/src/hdf5.o
CXX(target) Release/obj.target/hdf5/src/h5_file.o
CXX(target) Release/obj.target/hdf5/src/h5_group.o
SOLINK_MODULE(target) Release/obj.target/hdf5.node
COPY Release/hdf5.node
COPY /opt/test-project/node_modules/hdf5/lib/binding/hdf5.node
TOUCH Release/obj.target/action_after_build.stamp
CXX(target) Release/obj.target/h5ds/src/h5ds.o
SOLINK_MODULE(target) Release/obj.target/h5ds.node
COPY Release/h5ds.node
CXX(target) Release/obj.target/h5im/src/h5im.o
SOLINK_MODULE(target) Release/obj.target/h5im.node
COPY Release/h5im.node
CXX(target) Release/obj.target/h5lt/src/h5lt.o
SOLINK_MODULE(target) Release/obj.target/h5lt.node
COPY Release/h5lt.node
CXX(target) Release/obj.target/h5pt/src/h5pt.o
CXX(target) Release/obj.target/h5pt/src/h5_pt.o
SOLINK_MODULE(target) Release/obj.target/h5pt.node
COPY Release/h5pt.node
CXX(target) Release/obj.target/h5tb/src/h5tb.o
SOLINK_MODULE(target) Release/obj.target/h5tb.node
COPY Release/h5tb.node
make: Leaving directory '/opt/test-project/node_modules/hdf5/build'
gyp info ok
node-pre-gyp info ok
npm info postinstall [email protected]
[email protected] node_modules/hdf5
npm info ok
from hdf5.node.
duckontheweb
commented on July 22, 2024
What flavor of Linux are you using? Maybe I can try on a different distro and see if I can get it to work that way.
from hdf5.node.
rimmartin
commented on July 22, 2024
Ubuntu and CentOS. I'll be at a mac this morning and testing it there
from hdf5.node.
zszszsz
commented on July 22, 2024
I guess you have no hdf5 lib installed?
from hdf5.node.
rimmartin
commented on July 22, 2024
gcc (Debian 4.9.2-10) 4.9.2
is really a clang toolchain installed on your mac? It isn't a gcc installed by homebrew or compiled there?
My mac is older 10.7 and it has gcc compiled and built on it because the clang was too old and the other software of my company is gcc portable.
But up further it looked like npm install hdf5 --fallback-to-build --hdf5_home_mac=/usr/local/hdf5 did install and build. you don't want the --hdf5_home_linux because you'll get *.so dependency.
In your /usr/local/hdf5/lib folder are the dynamic libraries *.so or *.dylib? Needs to be *.dylib
from hdf5.node.
duckontheweb
commented on July 22, 2024
Thanks for helping me troubleshoot this. Just wanted to be clear again that I am running this is on Linux and not on a Mac.
The HDF5 library installs successfully and passes all make check and make check-install tests and is located at /usr/local/hdf5. I think I had not cleared my previous build properly the first time I tried installing with the --hdf5_home_mac flag, which is why the build appeared to be successful. When I fully removed the hdf5.node install and started over I got the error noted a few posts ago that it could not find hdf5.h.
It looks like all of the dynamic libraries in /usr/local/hdf5/lib are in fact *.so. I've been following the HDF5 in section 2.1 of this HDF5 documentation to install the HDF5 libraries. Is there something I should do differently to get *.dylib extensions on a Linux machine?
I should also mention that these HDF5 libraries are working with the Python module h5py without issue on this machine.
from hdf5.node.
duckontheweb
commented on July 22, 2024
Okay, I think I finally got it.
I was confused by the "Environment Variables" section of the documentation, which said to use add this at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./hdf5.node/../hdf5/lib
I couldn't find the hdf5.node directory anywhere on my file system, and I wasn't sure if I was supposed to be adding a path to something inside of the hdf5 node module or to something in the C libraries. This was the command that worked for me:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_HDF5_installation>/lib
which in my case is
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/hdf5/lib
What is the "hdf.node" portion of that path in the documentation supposed to be pointing to?
from hdf5.node.
rimmartin
commented on July 22, 2024
Sorry, I mistook this as a mac build issue
from hdf5.node.
rimmartin
commented on July 22, 2024
npm install hdf5 --fallback-to-build --hdf5_home_linux=/usr/local/hdf5
build is good
Next do you have /usr/local/hdf5/lib on your LD_LIBRARY_PATH?
from hdf5.node.
rimmartin
commented on July 22, 2024
"hdf.node" is the actual name of this project in github
https://github.com/HDF-NI/hdf5.node
I'll revise the documentation to put in your more clear wording
from hdf5.node.
Related Issues (20)
- Support for Single Writer Multiple Reader (SWMR)? HOT 7
- Getting dataset attribute (getDatasetAttribute) on a 32 bit floating point in NODE/javascript returns a totally different value HOT 6
- hdf5_home_win does not get set HOT 2
- Read dataset with 2d array stored fails on reading chunks HOT 10
- issues reading 4 dimensional dataset HOT 2
- SyntaxError: unsupported data type on compound datasets HOT 5
- Node 12? HOT 32
- Delete attribute HOT 6
- Tutorial: "Writing & Reading subsets" is not working. HOT 3
- Segfault reading HOT 4
- issue with appending to tables on windows 10
- Error: The specified procedure could not be found. (process.dlopen) HOT 1
- `hdf5.File is not a constructor` when bundled with webpack HOT 2
- cannot install HOT 3
- Win10+Node v14.15.5 Compilation errors HOT 6
- Getting data from Buffer
- Compile Error HOT 12
- install with yarn? HOT 2
- windows-build-tools / vs2017? HOT 37
- Error with handling variable length data (H5T_VLEN) HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hdf5.node.