I am trying to install OpenMPI on a new install of RHEL 9.1, and keep getting this error while using mock:
RPM build errors:
error: Bad exit status from /var/tmp/rpm-tmp.6QyYma (%build)
Macro expanded in comment on line 708: %{install_in_opt}, then we're instaling OMPI to
Bad exit status from /var/tmp/rpm-tmp.6QyYma (%build)
Full output here. Generated from $ mock -r rhel-9-x86_64 rebuild openmpi-4.1.4-1.src.rpm. Not sure if it changes things, but I did do $ mock -r rhel-9-x86_64 --init beforehand as well.
I got a src.rpm from the OpenMPI download page, and because I did not know how to install it, used this and this, as well as the epel docs to help me along the process. I changed any rhel or epel 7 references to 9, and during installation/initialization for mock, everything seemed to work alright (as far as I could tell).
Coming from Ubuntu, I previously used the deprecated mpif90 to compile mpi stuff, but I believe I was able to install that using a package. I now want to use mpifort. Is there a better/different way to install the mpifort compiler wrapper, or a problem with my installation process? Is it not supported currently, and should I install legacy support of some kind?
I am trying to run an app but I get
...
/usr/lib64/libstdc++.so.6: VERSION 'GLIBCXX_3.4.15' not found
/lib64/libc.so.6: VERSION 'GLIBC_2.15' not found
/lib64/libc.so.6: VERSION 'GLIBC_2.14' not found
...
When I do "strings /usr/lib64/libstdc++.so.6 | grep GLIBC" i get a normal list...
...
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
...
GLIBCXX_3.4.13
GLIBCXX_2.2.5
GLIBCXX_2.3.2
...
I don't seem to find a simple tutorial on how to install the missing libs/files/dependencies, (or Centos 6.5 or anything else for that mater).
Can someone explain how to install whatever might be missing on Centos?
Can someone explain how to install whatever might be missing on Centos?
You need glibc >= 2.15 and libstdc++ >= 3.4.15.
In theory, installing e.g. glibc-2.19 on the system should work (glibc provides backward binary compatibility), but this message suggests that you would not find a standard package for your OS with such an upgrade.
Instead you would have to either install a second version of glibc, as documented here, and redirect your application to use that version by binary-patching the loader encoded into the application, or run your application in a chroot (where you can install any version of glibc you like).
Similar considerations apply to libstdc++.so.6 as well, except you don't have to install it into the fixed location -- you can install newer copy anywhere, and point LD_LIBRARY_PATH to it.
Your final (and most likely easiest) alternative is to build the app you are trying to run from source, or obtain a pre-built binary for your distribution (one that doesn't require newer libraries than what you have).
When attempting to compile RNNLib, I got an error in NetcdfDataset.hpp:26:24 saying that Netcdfcpp.h could not be found. I looked around and found a bug report from 2011 that suggested that this was a bug, but it claimed to have been fixed. I have tried everything I can think of, including rebuilding NetCDF (a dependency of RNNLib) with various different flags, and have been unable to fix this bug. Can anyone give me a hand?
I had some trouble on a virtual machine building rnnlib.
I had to install the C and C++ version of NetCDF to get it to work.
The C version can be installed via sudo apt-get install libnetcdf-dev
I had to install the C++ version by building it.
Hope it will help. It's quite a difficult lib to install.
Maybe this helps someone: you can avoid some of the pain by installing packages from APT, and access the correct version mentioned by user3620756, which contains the netcdfcpp.h header file
. This happens through a legacy package, available on Ubuntun 16.04 (Xenial universe, see APT repository).
First install libnetcdf for C, then install libnetcdf-cxx-legacy-dev which should depend on libnetcdf-c++4 and install required C++ libraries on the go:
sudo apt install libnetcdf-dev libnetcdf-cxx-legacy-dev
The newest version doesn't have this netcdfcpp.h file anymore.
I had to use ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx-4.2.tar.gz to get it working.
I have also followed the same process and it worked for me
"The newest version doesn't have this netcdfcpp.h file anymore. I had to use ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx-4.2.tar.gz to get it working."
After downloading the folder, I had to build it by entering into the netcdf folder. I used simple command for the task :
.\configure
make
sudo make install
But in the file named as "NetcdfDataset.hpp", I have to give the complete path of the netcdfcpp.h file. For my case the path of the include file is :
#include "/Volumes/Macintosh_HD_2/WordSpottingProj/trunk/CODE C++/rnnlib_source_forge_version/netcdf-cxx-4.2/cxx/netcdfcpp.h"
I had this problem in the context of trying to use a makefile that called for netcdfcpp.h:
$ make -f makefile_MAC
c++ -O2 -o burn7.x burn7.cpp -I/opt/local/include -L/opt/local/lib -lm -lnetcdf_c++
burn7.cpp:31:10: fatal error: 'netcdfcpp.h' file not found
#include <netcdfcpp.h>
^
1 error generated.
make: *** [burn7.x] Error 1
I'm on a Mac, so I used Homewbrew to install the NetCDF package, but version 4.3.3.1 didn't appear to have netcdfcpp.h:
brew install homebrew/science/netcdf
However, I found that installing it with an additional flag resulted in this version being included:
brew install homebrew/science/netcdf --with-cxx-compat
I assume that the same is true of other installation/compilation methods, and not that this file has been taken out of versions since 4.2 as others answers state. Maybe it was a default option before and now it isn't?
I would like to install the older version of Google Protocol Buffers (protobuf-2.4.1) on Mac using the command line/Terminal app.
I tried with brew install protobuf, but the latest version 2.5.0 has been installed.
Is it possible to install the older version from the terminal?
There are some issues with building protobuf 2.4.1 from source on a Mac. There is a patch that also has to be applied. All this is contained within the homebrew protobuf241 formula, so I would advise using it.
To install protocol buffer version 2.4.1 type the following into a terminal:
brew tap homebrew/versions
brew install protobuf241
If you already have a protocol buffer version that you tried to install from source, you can type the following into a terminal to have the source code overwritten by the homebrew version:
brew link --force --overwrite protobuf241
Check that you now have the correct version installed by typing:
protoc --version
It should display 2.4.1
This is not via brew, but the end result is the same.
Download the protobuf-2.4.1 from https://github.com/protocolbuffers/protobuf/releases/tag/v2.4.1
Extract the tar.gz file.
$cd ~/Downloads/protobuf-2.4.1
$./configure
$make
$make check
$sudo make install
$which protoc
$protoc --version
Steps 4-7 are from the README.txt file from the protobuf tarball.
If you landed here looking for how to install Protocol Buffers on Mac, it can be done using Homebrew by running the command below
brew install protobuf
It installs the latest version of protobuf available. For me, at the time of writing, this installed the v3.7.1
If you'd like to install an older version, please look up the available ones from the package page Protobuf Package - Homebrew and install that specific version of the package.
The oldest available protobuf version in this package is v3.6.1.3
It's a new year and there's a new mismatch between the version of protobuf in Homebrew and the cutting edge release. As of February 2016, brew install protobuf will give you version 2.6.1.
If you want the 3.0 beta release instead, you can install it with:
brew install --devel protobuf
For some reason I need to use protobuf 2.4.1 in my project on OS X El Capitan. However homebrew has removed protobuf241 from its formula. I install it according #kksensei's answer manually and have to fix some error during the process.
During the make process, I get 3 error like following:
google/protobuf/message.cc:130:60: error: implicit instantiation of undefined template 'std::__1::basic_istream<char, std::__1::char_traits<char> >'
return ParseFromZeroCopyStream(&zero_copy_input) && input->eof();
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:108:28: note: template is declared here
class _LIBCPP_TYPE_VIS basic_istream;
^
google/protobuf/message.cc:135:67: error: implicit instantiation of undefined template 'std::__1::basic_istream<char, std::__1::char_traits<char> >'
return ParsePartialFromZeroCopyStream(&zero_copy_input) && input->eof();
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:108:28: note: template is declared here
class _LIBCPP_TYPE_VIS basic_istream;
^
google/protobuf/message.cc:175:16: error: implicit instantiation of undefined template 'std::__1::basic_ostream<char, std::__1::char_traits<char> >'
return output->good();
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:110:28: note: template is declared here
class _LIBCPP_TYPE_VIS basic_ostream;
^
(Sorry, I dont know how to attach code when the code contains '`' )
If you get the same error, please edit src/google/protobuf/message.cc, add #include <istream> at the top of the file and do $ make again and should get no errors. After that do $ sudo make install. When install finished $protoc --version should display the correct result.
From https://github.com/paulirish/homebrew-versions-1 . Works for me!
brew install https://raw.githubusercontent.com/paulirish/homebrew-versions-1/master/protobuf241.rb
I used macports
sudo port install protobuf-cpp
To install Protocol Buffer (as of today version v3.7.0)
Go to this website
download the zip file according to your OS (e.g.: protoc-3.7.0-osx-x86_64.zip). This applies also to other OS.
Move the executable in protoc-3/bin/protoc to one of your directories in PATH. In Mac I suggest to put it into /usr/local/bin
Now your good to go 💪🏾
(optional) There is also an include file, you can add. This is a snippet of the README.md
If you intend to use the included well known types then don't forget to
copy the contents of the 'include' directory somewhere as well, for example
into '/usr/local/include/'.
Please refer to our official github site for more installation instructions:
https://github.com/protocolbuffers/protobuf
brew install --devel protobuf
If it tells you "protobuf-2.6.1 already installed":
1. brew uninstall --devel protobuf
2. brew link libtool
3. brew install --devel protobuf
There is another official way by Google, as mentioned by another user.
Read it fully before trying.
Here are the steps:
Open Terminal and type the following
PROTOC_ZIP=protoc-3.7.1-osx-x86_64.zip
curl -OL https://github.com/google/protobuf/releases/download/v3.7.1/$PROTOC_ZIP
sudo unzip -o $PROTOC_ZIP -d /usr/local bin/protoc
rm -f $PROTOC_ZIP
Worked for me.
P.S.
This is for version 3.7.1 in osx only.
If you want to install some other version/platform, visit the releases link and check out the details of the latest version, and use those information.
Reference
FWIW., the latest version of brew is at protobuf 3.0, and doesn't include any formulae for the older versions. This is somewhat "inconvenient".
While protobuf may be compatible at the wire level, it is absolutely not compatible at the level of generated java classes: you can't use .class files generated with protoc 2.4 with the protobuf-2.5 JAR, etc. etc. This is why updating protobuf versions is such a sensitive topic in the Hadoop stack: it invariably requires coordination across different projects, and is traumatic enough that nobody likes to do it.
HomeBrew versions has been removed and formulaes have been emptied. Therefore, my advice is to install it manually following the following steps.
For the time being you will need to build and install the Protocol Buffers toolset manually.
Download source code: https://github.com/google/protobuf/releases/download/v2.4.1/protobuf-2.4.1.tar.gz
tar xvfz protobuf-2.4.1.tar.gz
cd protobuf-2.4.1
Run ./configure
Edit src/google/protobuf/message.cc, add #include at the top of the file
Run make command from root of the folder, i.e. protobuf-2.4.1/
Run sudo make install
Run /usr/local/bin/protoc --version to check the version of protobuf compiler version
The terminal output should be:
Version: libprotoc 2.4.1
you can install from official link page provided by google http://google.github.io/proto-lens/installing-protoc.html
For v3 users.
http://google.github.io/proto-lens/installing-protoc.html
PROTOC_ZIP=protoc-3.7.1-osx-x86_64.zip
curl -OL https://github.com/protocolbuffers/protobuf/releases/download/v3.7.1/$PROTOC_ZIP
sudo unzip -o $PROTOC_ZIP -d /usr/local bin/protoc
sudo unzip -o $PROTOC_ZIP -d /usr/local 'include/*'
rm -f $PROTOC_ZIP
There should be better ways but what I did today was:
Download from https://github.com/protocolbuffers/protobuf/releases (protoc-3.14.0-osx-x86_64.zip at this moment)
Unzip (double click the zip file)
Here, I added a symbolic link
ln -s ~/Downloads/protoc-3.14.0-osx-x86_64/bin/protoc /usr/local/bin/protoc
Check if works
protoc --version
After making cabal install of the darcsden code I get this message:
cabal: The following packages are likely to be broken by the reinstalls:
bin-package-db-0.0.0.0
ghc-7.4.1
Use --force-reinstalls if you want to install anyway.
How do I get around this? What does it mean?
Why does it happen?
If you look at the full output of cabal install darcsden, you will find several lines that look like this:
binary-0.5.1.0 -bytestring-in-base (reinstall) changes: array-0.4.0.0 ->
0.3.0.3, containers-0.4.2.1 -> 0.4.1.0
This means that cabal has found an install plan that involves (destructively) reinstalling packages that you already have on your system.
Now, GHC packages are rather sensitive when it comes to their (reflexive) dependencies, and generally only work if exactly the right version of all dependencies is available, compiled against the right versions of their dependencies and so on. Therefore, replacing an already installed package with a new version of changed dependencies can cause some packages on your system to become unusable. Since version 0.14.0, cabal warns you about such a situation in advance to prevent you from accidentally breaking your system.
In your case, ghc and bin-package-db are among the potentially broken packages, because they depend on binary which gets reinstalled. So you should not try to use the --force-reinstalls flag, because it might really break your GHC.
What can you do?
If you scan what is going to be reinstalled, you see that quite a few dependencies are downgraded. This hints at the fact that the package you are trying to install might not be properly updated to GHC 7.4.1 yet.
You can in general try to call cabal install darcsden --avoid-reinstalls to explicitly try to find an install plan that has no reinstalls. Unfortunately, in this case, it fails (for me).
I've briefly looked at the darcsden package description, but it looks like quite a few dependencies of darcsden need to be updated. So the remaining options are: Convince the author(s) of darcsden to release an updated version, or install darcsden using an older version of GHC (such as 7.0.4), which should just work.