I am trying to install ipopt by:
brew install ipopt.rb --with-openblas
and I got the following error:
==> Installing dependencies for ipopt: mumps
==> Installing ipopt dependency: mumps
==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
Already downloaded: /Users/yufeiliu/Library/Caches/Homebrew/mumps-5.1.1.tar.gz
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.
Last 15 lines from /Users/yufeiliu/Library/Logs/Homebrew/mumps/01.make:
clang -fPIC -I../include -O -c symbfac.c -o symbfac.o
clang -fPIC -I../include -O -c interface.c -o interface.o
clang -fPIC -I../include -O -c sort.c -o sort.o
clang -fPIC -I../include -O -c minpriority.c -o minpriority.o
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then \
cp ./PORD/lib//libpord.dylib lib/libpord.dylib; \
fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2
If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues
Does anyone know how to solve this?
Unfortunately installation of mumps package with brew is very problematic at this moment. You have two different ways to install mumps
Method 1:
brew tap brewsci/science
brew install mumps
if that didn't work, download mumps.rb from here
brew install ./mumps.rb
Method 2
brew tap dpo/openblas
brew install mumps
The second method might lead to some issues with scalapack later.
Update: Unfortunately the above method might not work properly anymore. I have updated the installation method here.
Related
I've been trying to build open3d from source on the l4t-base:r32.5.0 IMG from NVIDIA for quite some time now and have basically searched the whole internet for a script/guide, but I can't seem to find anything or get it to work myself.
Following the exact steps stated on http://www.open3d.org/docs/release/arm.html I get the following output while running the following Dockerfile
Dockerfile
FROM dustynv/ros:foxy-ros-base-l4t-r32.5.0
WORKDIR /workspace
##########################
### CMAKE INSTALLATION ###
##########################
RUN wget https://github.com/Kitware/CMake/releases/download/v3.20.6/cmake-3.20.6-linux-aarch64.tar.gz
RUN tar -v -xzf cmake-3.20.6-linux-aarch64.tar.gz
RUN mv cmake-3.20.6-linux-aarch64 cmake
RUN echo "alias cmake='/workspace/cmake/bin/cmake'" >> /root/.bashrc
RUN source /root/.bashrc && cmake --version
#################################
### OPEN3D 0.13.0 INSTALLTION ###
#################################
RUN wget https://github.com/isl-org/Open3D/archive/refs/tags/v0.13.0.tar.gz
RUN tar -v -xzf v0.13.0.tar.gz
RUN mv Open3D-0.13.0 open3d
RUN apt-get update && apt-get install xorg-dev libglu1-mesa-dev -y
RUN cd open3d && mkdir build && cd build && \
/workspace/cmake/bin/cmake \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS=ON \
-DBUILD_CUDA_MODULE=OFF \
-DBUILD_GUI=OFF \
-DBUILD_TENSORFLOW_OPS=OFF \
-DBUILD_PYTORCH_OPS=OFF \
-DBUILD_UNIT_TESTS=ON \
-DCMAKE_INSTALL_PREFIX=~/open3d_install \
-DPYTHON_EXECUTABLE=/usr/bin/python3 \
..
ErrorLog
Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /workspace/open3d/build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make -f Makefile cmTC_d15b1/fast && /usr/bin/make -f CMakeFiles/cmTC_d15b1.dir/build.make CMakeFiles/cmTC_d15b1.dir/build
make[1]: Entering directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_d15b1.dir/src.c.o
/usr/bin/cc -DCMAKE_HAVE_LIBC_PTHREAD -fPIE -o CMakeFiles/cmTC_d15b1.dir/src.c.o -c /workspace/open3d/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_d15b1
/workspace/cmake/bin/cmake -E cmake_link_script CMakeFiles/cmTC_d15b1.dir/link.txt --verbose=1
/usr/bin/cc CMakeFiles/cmTC_d15b1.dir/src.c.o -o cmTC_d15b1
CMakeFiles/cmTC_d15b1.dir/src.c.o: In function `main':
src.c:(.text+0x48): undefined reference to `pthread_create'
src.c:(.text+0x50): undefined reference to `pthread_detach'
src.c:(.text+0x58): undefined reference to `pthread_cancel'
src.c:(.text+0x64): undefined reference to `pthread_join'
src.c:(.text+0x74): undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_d15b1.dir/build.make:98: recipe for target 'cmTC_d15b1' failed
make[1]: *** [cmTC_d15b1] Error 1
make[1]: Leaving directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_d15b1/fast' failed
make: *** [cmTC_d15b1/fast] Error 2
Source file was:
#include <pthread.h>
static void* test_func(void* data)
{
return data;
}
int main(void)
{
pthread_t thread;
pthread_create(&thread, NULL, test_func, NULL);
pthread_detach(thread);
pthread_cancel(thread);
pthread_join(thread, NULL);
pthread_atfork(NULL, NULL, NULL);
pthread_exit(NULL);
return 0;
}
Looking for a ASM_NASM compiler failed with the following output:
-- The ASM_NASM compiler identification is unknown
-- Didn't find assembler
CMake Error at CMakeLists.txt:2 (project):
No CMAKE_ASM_NASM_COMPILER could be found.
Tell CMake where to find the compiler by setting either the environment
variable "ASM_NASM" or the CMake cache entry CMAKE_ASM_NASM_COMPILER to the
full path to the compiler, or to the compiler name if it is in the PATH.
-- Configuring incomplete, errors occurred!
See also "/workspace/open3d/build/CMakeFiles/CheckASM_NASM/CMakeFiles/CMakeOutput.log".
See also "/workspace/open3d/build/CMakeFiles/CheckASM_NASM/CMakeFiles/CMakeError.log".
Determining if the function sgemm_ exists failed with the following output:
Change Dir: /workspace/open3d/build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make -f Makefile cmTC_855e0/fast && /usr/bin/make -f CMakeFiles/cmTC_855e0.dir/build.make CMakeFiles/cmTC_855e0.dir/build
make[1]: Entering directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_855e0.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=sgemm_ -fPIE -o CMakeFiles/cmTC_855e0.dir/CheckFunctionExists.c.o -c /workspace/cmake/share/cmake-3.20/Modules/CheckFunctionExists.c
Linking C executable cmTC_855e0
/workspace/cmake/bin/cmake -E cmake_link_script CMakeFiles/cmTC_855e0.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=sgemm_ CMakeFiles/cmTC_855e0.dir/CheckFunctionExists.c.o -o cmTC_855e0
CMakeFiles/cmTC_855e0.dir/CheckFunctionExists.c.o: In function `main':
CheckFunctionExists.c:(.text+0x10): undefined reference to `sgemm_'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_855e0.dir/build.make:98: recipe for target 'cmTC_855e0' failed
make[1]: *** [cmTC_855e0] Error 1
make[1]: Leaving directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_855e0/fast' failed
make: *** [cmTC_855e0/fast] Error 2
Determining if the function cheev_ exists failed with the following output:
Change Dir: /workspace/open3d/build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make -f Makefile cmTC_3a46a/fast && /usr/bin/make -f CMakeFiles/cmTC_3a46a.dir/build.make CMakeFiles/cmTC_3a46a.dir/build
make[1]: Entering directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_3a46a.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=cheev_ -fPIE -o CMakeFiles/cmTC_3a46a.dir/CheckFunctionExists.c.o -c /workspace/cmake/share/cmake-3.20/Modules/CheckFunctionExists.c
Linking C executable cmTC_3a46a
/workspace/cmake/bin/cmake -E cmake_link_script CMakeFiles/cmTC_3a46a.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=cheev_ CMakeFiles/cmTC_3a46a.dir/CheckFunctionExists.c.o -o cmTC_3a46a /usr/lib/aarch64-linux-gnu/libblas.so -pthread -lm -ldl
CMakeFiles/cmTC_3a46a.dir/CheckFunctionExists.c.o: In function `main':
CheckFunctionExists.c:(.text+0x10): undefined reference to `cheev_'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_3a46a.dir/build.make:99: recipe for target 'cmTC_3a46a' failed
make[1]: *** [cmTC_3a46a] Error 1
make[1]: Leaving directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_3a46a/fast' failed
make: *** [cmTC_3a46a/fast] Error 2
Determining if the function LAPACKE_dgeqrf exists failed with the following output:
Change Dir: /workspace/open3d/build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make -f Makefile cmTC_9905d/fast && /usr/bin/make -f CMakeFiles/cmTC_9905d.dir/build.make CMakeFiles/cmTC_9905d.dir/build
make[1]: Entering directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_9905d.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=LAPACKE_dgeqrf -fPIE -o CMakeFiles/cmTC_9905d.dir/CheckFunctionExists.c.o -c /workspace/cmake/share/cmake-3.20/Modules/CheckFunctionExists.c
Linking C executable cmTC_9905d
/workspace/cmake/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9905d.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=LAPACKE_dgeqrf CMakeFiles/cmTC_9905d.dir/CheckFunctionExists.c.o -o cmTC_9905d /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so
CMakeFiles/cmTC_9905d.dir/CheckFunctionExists.c.o: In function `main':
CheckFunctionExists.c:(.text+0x10): undefined reference to `LAPACKE_dgeqrf'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_9905d.dir/build.make:100: recipe for target 'cmTC_9905d' failed
make[1]: *** [cmTC_9905d] Error 1
make[1]: Leaving directory '/workspace/open3d/build/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_9905d/fast' failed
make: *** [cmTC_9905d/fast] Error 2
Problem:
I want to build open3d from source on an arm docker img with a Dockerfile. More specifically, the l4t-base:r32.5.0 img provided by NVIDIA. This image will be used on a Jetson XavierNX with docker installed.
Above you can see what I have tried so far in terms of Dockerfile and the output this gives me.
What I am asking is, if anyone has a Dockerfile for building open3d from source on an arm based image or knows how to do it successfully, because I cannot seem to be able to do it.
I have installed mosquitto using the command apt-get install mosquitto. It is installed successfully on my system, but I got version "1.4.5". I want to downgrade to version 1.4.4, so I was trying using the source tar file. Under folder, I am running the command make and it is throwing an error:
set -e; for d in lib client src; do make -C ${d}; done
make[1]: Entering directory `/home/ubuntu/org.eclipse.mosquitto-1.4.4/lib'
cc -Wall -ggdb -O2 -I. -I.. -I../lib -fPIC -DWITH_TLS -DWITH_TLS_PSK -DWITH_THREADING -DWITH_SOCKS -DWITH_SRV -c mosquitto.c -o mosquitto.o
In file included from mosquitto.c:33:0:
./mosquitto_internal.h:27:27: fatal error: openssl/ssl.h: No such file or directory
# include <openssl/ssl.h>
^
compilation terminated.
make[1]: *** [mosquitto.o] Error 1
make[1]: Leaving directory `/home/ubuntu/org.eclipse.mosquitto-1.4.4/lib'
make: *** [mosquitto] Error 2
What is going wrong here?. Is there any another way to install 1.4.4 version of mosquitto?
Thanks
You're missing dependencies needed for compilation.
Try:
apt-get install libc-ares-dev libssl-dev libwrap0-dev uthash-dev uuid-dev
If you want libwebsockets support you can either install libwebsockets-dev, or better install it manually from source - that will get you version 1.5 instead of the old 1.2 that is in Debian/Ubuntu.
If you install the manually compiled version with
make prefix=/usr install
then it will overwrite the existing binary and you can use it with the existing system services.
Getting an error when I try to install dos2unix via homebrew. brew doctor has no suggestions, and other install work like a charm. No idea where to start tracing it.
$ brew install dos2unix
==> Downloading http://waterlan.home.xs4all.nl/dos2unix/dos2unix-6.0.3.tar.gz
Already downloaded: /Library/Caches/Homebrew/dos2unix-6.0.3.tar.gz
==> make prefix=/usr/local/Cellar/dos2unix/6.0.3 CC=cc CPP=cc CFLAGS= CFLAGS_OS=
cc -DVER_REVISION=\"6.0.3\" -DVER_DATE=\"2013-01-25\" -DVER_AUTHOR=\"'Erwin Waterlander'\" -DDEBUG=0 -I/usr/local/Cellar/gettext/0.18.3.1/include -DD2U_UNICODE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DENABLE_NLS -DLOCALEDIR=\"/usr/local/Cellar/dos2unix/6.0.3/share/locale\" -DPACKAGE=\"dos2unix\" -c unix2dos.c -o unix2dos.o
pod2text man/man1/dos2unix.pod > man/man1/dos2unix.txt
/bin/sh: /usr/bin/pod2text: Permission denied
make: *** [man/man1/dos2unix.txt] Error 126
make: *** Waiting for unfinished jobs....
On my system /usr/bin/pod2text had no execution rights. After changing that by executing the following command I had no problem installing dos2unix:
sudo chmod +x /usr/bin/pod2text
Pretty much what it sounds like. I did:
brew install imagemagick
That seemed to go well--so the problem is not with imagemagick itself.
I then tried to install the PHP extension (updating pear and pecl before trying):
pecl install imagick
It fails. Here's what happens near the end:
running: make
/bin/sh /private/tmp/pear/install/pear-build-brad.garrettZppuRq/imagick-3.0.1/libtool --mode=compile cc -I. -I/private/tmp/pear/install/imagick -DPHP_ATOM_INC -I/private/tmp/pear/install/pear-build-brad.garrettZppuRq/imagick-3.0.1/include -I/private/tmp/pear/install/pear-build-brad.garrettZppuRq/imagick-3.0.1/main -I/private/tmp/pear/install/imagick -I/usr/include/php -I/usr/include/php/main -I/usr/include/php/TSRM -I/usr/include/php/Zend -I/usr/include/php/ext -I/usr/include/php/ext/date/lib -DHAVE_CONFIG_H -g -O2 -c /private/tmp/pear/install/imagick/imagick_class.c -o imagick_class.lo
mkdir .libs
cc -I. -I/private/tmp/pear/install/imagick -DPHP_ATOM_INC -I/private/tmp/pear/install/pear-build-brad.garrettZppuRq/imagick-3.0.1/include -I/private/tmp/pear/install/pear-build-brad.garrettZppuRq/imagick-3.0.1/main -I/private/tmp/pear/install/imagick -I/usr/include/php -I/usr/include/php/main -I/usr/include/php/TSRM -I/usr/include/php/Zend -I/usr/include/php/ext -I/usr/include/php/ext/date/lib -DHAVE_CONFIG_H -g -O2 -c /private/tmp/pear/install/imagick/imagick_class.c -fno-common -DPIC -o .libs/imagick_class.o
In file included from /private/tmp/pear/install/imagick/imagick_class.c:21:
/private/tmp/pear/install/imagick/php_imagick.h:49:12: fatal error: 'wand/MagickWand.h' file not found
# include <wand/MagickWand.h>
^
1 error generated.
make: *** [imagick_class.lo] Error 1
ERROR: `make' failed
Any ideas?? This is only the umpteenth time I've had issues installing imagemagick on a computer. Seems they change little things here and there all the time (for instance, I've never heard of "magickwand" before now).
I complied ImageMagick according to http://www.imagemagick.org/script/install-source.php#unix
Then I followed http://verysimple.com/2011/12/21/install-image-magick-for-php-on-osx/
Had the following error fatal error: 'wand/MagickWand.h' file not found
Then I found http://www.imagemagick.org/discourse-server/viewtopic.php?f=10&t=22644
Had to find the solution in config.m4, it was exporting pkgconfig:
export PKG_CONFIG_PATH="`MagickWand-config --prefix`/lib/pkgconfig/"
Then I configured with the following:
LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include" ./configure --with-imagick=/usr/local
I had installed ImageMagick on my local server and it worked perfectly fine. But when I moved to webfaction, and tried installing it on the server I had issues. The ImageMagick is installed on the server but I am not able to install the php extension imagick. I followed the steps and downloaded the tar file from http://pecl.php.net/get/imagick-3.0.1.tgz. I then unzipped the file and its contents and configured it. I also did phpize. But when I did make I got the following errors:
[e#web308 imagick-3.0.1]$ make
/bin/sh /home/e/temp/imagick-3.0.1/libtool --mode=compile cc -I. -I/home/e/temp/imagick-3.0.1 -DPHP_ATOM_INC -I/home/e/temp/imagick-3.0.1/include -I/home/e/temp/imagick-3.0.1/main -I/home/e/temp/imagick-3.0.1 -I/usr/local/include/php54 -I/usr/local/include/php54/main -I/usr/local/include/php54/TSRM -I/usr/local/include/php54/Zend -I/usr/local/include/php54/ext -I/usr/local/include/php54/ext/date/lib -I/usr/include/ImageMagick -DHAVE_CONFIG_H -g -O2 -c /home/e/temp/imagick-3.0.1/imagick_class.c -o imagick_class.lo
mkdir .libs
cc -I. -I/home/e/temp/imagick-3.0.1 -DPHP_ATOM_INC -I/home/e/temp/imagick-3.0.1/include -I/home/e/temp/imagick-3.0.1/main -I/home/e/temp/imagick-3.0.1 -I/usr/local/include/php54 -I/usr/local/include/php54/main -I/usr/local/include/php54/TSRM -I/usr/local/include/php54/Zend -I/usr/local/include/php54/ext -I/usr/local/include/php54/ext/date/lib -I/usr/include/ImageMagick -DHAVE_CONFIG_H -g -O2 -c /home/e/temp/imagick-3.0.1/imagick_class.c -fPIC -DPIC -o .libs/imagick_class.o
/home/e/temp/imagick-3.0.1/imagick_class.c: In function ‘zim_imagick_setfont’:
/home/e/temp/imagick-3.0.1/imagick_class.c:1442: error: ‘struct _php_core_globals’ has no member named ‘safe_mode’
/home/e/temp/imagick-3.0.1/imagick_class.c:1442: error: ‘CHECKUID_CHECK_FILE_AND_DIR’ undeclared (first use in this function)
/home/e/temp/imagick-3.0.1/imagick_class.c:1442: error: (Each undeclared identifier is reported only once
/home/e/temp/imagick-3.0.1/imagick_class.c:1442: error: for each function it appears in.)
/home/e/temp/imagick-3.0.1/imagick_class.c:1442: error: ‘CHECKUID_NO_ERRORS’ undeclared (first use in this function)
/home/e/temp/imagick-3.0.1/imagick_class.c: In function ‘zim_imagick_setimageprogressmonitor’:
/home/e/temp/imagick-3.0.1/imagick_class.c:9534: error: ‘struct _php_core_globals’ has no member named ‘safe_mode’
/home/e/temp/imagick-3.0.1/imagick_class.c:9534: error: ‘CHECKUID_CHECK_FILE_AND_DIR’ undeclared (first use in this function)
/home/e/temp/imagick-3.0.1/imagick_class.c:9534: error: ‘CHECKUID_NO_ERRORS’ undeclared (first use in this function)
make: *** [imagick_class.lo] Error 1
It says some of the variables are undeclared. I tried with other versions and get the same errors.
Any help on what I might be doing wrong here?
Thanks in advance.
PHP54 won't work with version 3.0.1 you can use the latest version to fix this:
wget http://pecl.php.net/get/imagick-3.1.0RC2.tgz
tar xzvf imagick-3.1.0RC2.tgz
cd imagick-3.1.0RC2
phpize
./configure
make
cp modules/imagick.so /your-php-extensions-directory-path/
The solution is to install the beta version of the module instead:
pear config-set preferred_state beta
pecl install imagick