I'm trying to install the TDA on my Mac. Prior to this I tried phom but it was, I guess, out of date.
It tells me
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘TDA’
Do you want to attempt to install these from sources?
then has a giant blob of red text after I accept, mentioning a whole bunch of files and saying
Warning: pragma diagnostic pop could not pop, no matching push
a number of times for each block of text, then
all paths through this function will call itself
and
fatal error: 'gmp.h' file not found
but I went into terminal and had it install gmp, but that failed for some reason or another. Something about not finding a working compiler
Please help I'm trying to do my final project. I'm a mathematician who loves math and is terrible with computers and I've been fighting with a computer for the last 3 days on various final projects and I can't wait to get done with my applied semester and just go back to pure math and I'm probably going to cry.
Related
With a colleague, we are working on this github repo. When I knit manuscript.Rmd, I get an error "Unable to load picture or PDF file 'nwr.by.freq.ITEM'." as in this commit. When she knits it, it works fine, as in this commit.
The error comes after all chunks have been done, so it's not a problem within R/RStudio. (Plus, we are using renv, and I already checked for discrepancies between versions of our R, Rstudio, and packages.) The problem must come from knitting, so in the pandoc stage or thereabouts.
Given that we have some phonetic symbols (which is why we need to generate the figure in a png, and then read it back in), we are using xelatex as our engine, as recommended here. I don't think these symbols are the problem -- but I do suspect the issue is a divergence between her latex engine and mine. I'm not totally sure how to check for that...
(I'll be trying to answer my own question, so you can just wait and see if I crack this alone!)
To begin with, I updated xelatex, which led to a missing apa6.cls error. Following papaja install instructions, I would ideally re-install mactex -- but while it downloads (since it takes 1h), I just installed tinytex with tinytex::install_tinytex(). At my first attempt to knit the document after that, tinytex downloaded many things. And then the knit went through! Problem solved.
I know how to code but I really do not know my way around a computer.
I have a program that I have to run for my master thesis. It is a code with multiple collabs and runs perfectly on Linux. However, it is a very complex simulational code and therefore it takes time to run for multiple parameters. I've been using my Linux at the university to run it but would like to run some of it on my personal computer (MAC OS). It works by using the R language to call upon c++ functions as follows (being filename a code on c++).
On a Rstudio script:
Sys.setenv("PKG_CPPFLAGS" = "-fopenmp -DPARALLEL")
system("rm filename.so")
system("rm filename.o")
system ("R CMD SHLIB filename.cpp")
dyn.load("filename.so")
After system ("R CMD SHLIB filename.cpp") I get error:
clang: error: unsupported option '-fopenmp'
make: *** [filename.o] Error 1
I've researched on the subject and found this
Enable OpenMP support in clang in Mac OS X (sierra & Mojave)
I've Installed LLVM, yet I do not know how to use it in this case.
How do I use it in this case?
Thank you in advance.
"Don't do it that way." Read up on R and Rcpp and use the proper tools (especially for packaging and/or compiling) which should pick up OpenMP where possible. In particular,
scan at least the Rcpp Introduction vignette
also look at the Rcpp Attributes vignette
"Just say no" to building the compilation commands by hand unless you know what you are doing with R and have read Writing R Extensions carefully a few times. It can be done, I used to show how in tutorials and workshops (see old slides from 12-15 years ago on my website) but we first moved to package inline which helps here, and later relied on the much better Rcpp Attributes.
Now, macOS has some extra hurdles in which tools work and which ones don't. The rcpp-devel mailing list may be of help, the default step is otherwise to consult the tutorial by James.
Edit: And of course if you "just want the above to work" try the obvious step of removing the part causing the error, i.e. use
Sys.setenv("PKG_CPPFLAGS" = "")
as your macOS box appears to have a compiler but not OpenMP (which, as I understand it, is the default thanks to some "surprising" default choices at Apple -- see the aforementioned tutorial for installation help.)
I have been trying to compile a basic tensorRT project on a desktop host -for now the source is literally just the following:
#include <nvinfer.h>
class Logger : nvinfer1::public ILogger
{
} glogger;
Upon running make, though, I receive the following message:
fatal error: nvinfer.h: No such file or directory #include <nvinfer.h>
The error is correct, too - I used locate to try to find it, but there's nothing on my machine that matches. I followed the install instructions for desktop installation of TensorRT 2.1 as described here: https://developer.nvidia.com/nvidia-tensorrt-download
So my question is, does anyone know where nvinfer.h is supposed to be? In other words, am I missing a needed package that contains it, or did I miss something else that's essential?
Small addendum: one thing I noticed is that libgie1 is not installed, and it was not included as a debian with the provided TensorRT download like the other packages such as gie-dev were.
Before using locate, if you recently added new files is a good practice to run sudo updatedb, if the file is on the pc you should see it after.
Anyway googling a bit it looks like the header your looking for is NvInfer.h, caps matters.
I am currently installing the HDF5 library, more precisely the hdf5-1.10.0-patch1, on Cygwin, as I want to use it with Fortran. Following the instructions from the hdfgroup website
(here is the link), I did the following:
./configure --enable-fortran
make > "out1_check.txt" 2> "warn1_check.txt" &
make check > "out2_check.txt" 2> "warn2_check.txt" &
The execution of the last command (make check) proceeds as it should, until it gets stuck. The process does not stop and something is happening (8-12% CPU are in use by sh.exe, already 39 hours of CPU time) but "out2_check.txt" looks like
Making check in src
...
[many successful checks]
...
============================
No need to test testlinks_env.sh again.
============================
============================
Testing testswmr.sh
Unfortunately, I do not have the output file from the first run of make check, but it did not contain more information on Testing testswmr.sh. There was never any error message.
So, what is this testswmr.sh, why does it get stuck and how can I finalize the installation process? Maybe I can skip the remaining checks and just proceed to make install?
Important note: an older version of HDF5 is already installed from the Cygwin repo. It does not seem to support Fortran however, so I decided to install the current version myself.
Available (and used) compilers are gcc and gfortran.
As far as I can tell, only Intel Fortran is supported on Windows. There is no Cygwin download here https://support.hdfgroup.org/HDF5/release/obtain518.html and I have never come across a report of experience for Cygwin/Fortran/HDF5.
Your options:
Use Intel Fortran
Use Linux or Mac
Sorry
I am Mac OS 10.11 (El Capitan) user. I used 4.6 and when I tried to build some simulation I always get "Simulation terminated with exit code: 139" and couldn’t do nothing at all with that. I thought that when I install 5.0 then everything will be fine, but now I get something like that:
Simulation terminated with exit code: 132
Working directory: /Users/JL_Data/omnetpp-5.0/samples/tictoc
Command line: tictoc -r 0 --debug-on-errors=false omnetpp.ini
Environment variables:
PATH=/Users/JL_Data/omnetpp-5.0/bin::/usr/bin:/bin:/usr/sbin:/sbin
DYLD_LIBRARY_PATH=/Users/JL_Data/omnetpp-5.0/lib::
OMNETPP_IMAGE_PATH=/Users/JL_Data/omnetpp-5.0/images
And when I tried open some simulation in terminal I get:
Illegal instruction: 4
Do you have some idea what can I do with that problem? I tried to find something on the internet, but after one day I do not get any idea.
If you need some more information, please let me know.
As it is right now, your question is not completely clear, since it requires one to be familiar with omnet++ and probably some experience installing and setting it up. However, let me make a couple guesses.
First, Illegal instruction. This usually occurs when the binary was built for an architecture different than the one it's being run on; e.g. when then SSE2 or AVX instructions are present in the binary code, but are missing on the CPU.
See, for example, this SO question:
Find which assembly instruction caused an Illegal Instruction error without debugging
There is also a question that discusses exactly your problem, namely, "Illegal instruction: 4" on OS X:
What is the "Illegal Instruction: 4" error and why does "-mmacosx-version-min=10.x" fix it?
Now, since omnet++ appears to be an open source project, I expect it to have a mailing list and / or an IRC channel. Indeed, here is the communications page on the official website that links to a Google Groups-based mailing list:
https://omnetpp.org/get-involved
https://groups.google.com/forum/#!forum/omnetpp
I advise you to get in touch with the developers with a thorough description of your problem, since the chances of them knowing the solution are significantly higher compared to the chances of there being a user on SO who has faced similar problems when installing an identical version of omnet++ on an identical version of Mac OS X.