Develop Reference

ECDSA Signature Verification Performance in Java

I am trying to calculate the performance of ECDSA signature verification in Java for secp521r1 curve.
I am getting around 3000 signature verification per second.
Adding my other work also, I tested with openssl speed command for secp521r1 curve, there I got around 9000 verification on my machine (40 cores). I tested with Golang also but the performance with secp521r1 is not good, though the performance with secp256r1 is great(28000 verification per second). I reached out to Golang community and found 256 is hand optimized but other curves are not.
I also tested with nodeJs to verify signature, there I got 9000 verification per second which is similar to Openssl. By checking the source code of nodeJs crypto module implementation, I found they are using openssl like implementation.
But I have to work on Java only, so reaching out to the community. Is this the usual result in Java or do we have any openssl like implementation in Java as well?
Dummy Code==========================
package dummy;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.math.BigInteger;
import java.security.InvalidAlgorithmParameterException;
import java.security.KeyFactory;
import java.security.NoSuchAlgorithmException;
import java.security.NoSuchProviderException;
import java.security.PrivateKey;
import java.security.PublicKey;
import java.security.Security;
import java.security.Signature;
import java.security.cert.CertificateException;
import java.security.cert.CertificateFactory;
import java.security.cert.X509Certificate;
import java.security.spec.PKCS8EncodedKeySpec;
import java.security.spec.X509EncodedKeySpec;
import java.util.Base64;
import org.bouncycastle.asn1.DERInteger;
import org.bouncycastle.asn1.DERSequence;
import org.bouncycastle.jce.provider.BouncyCastleProvider;
import org.bouncycastle.util.io.pem.PemObject;
import org.bouncycastle.util.io.pem.PemReader;
import org.json.JSONObject;
public class DSA {
static JSONObject ob = new JSONObject();
static byte[] strByte = null;
static byte[] realSig;
static String str = "a";//"{\"type\":\"issueTx\",\"userId\":1,\"transaction\":{\"amount\":1000}}"; /a
static byte[] sigdata;
static String sigEdata;
static X509Certificate c;
static String sigTestSigneddata;
public static void main(String[] args)
throws InvalidAlgorithmParameterException, NoSuchAlgorithmException, IOException {
try {
KeyPairGenerator keyGen = KeyPairGenerator.getInstance("EC");
keyGen.initialize(new ECGenParameterSpec("secp521r1"), new SecureRandom());
KeyPair pair = keyGen.generateKeyPair();
PrivateKey priv = pair.getPrivate();
PublicKey pub = pair.getPublic();
FileWriter fw = new FileWriter("MyKeys/n.pem");
PemWriter writer = new PemWriter(fw);
writer.writeObject(new PemObject("PUBLIC KEY", pub.getEncoded()));
writer.close();
FileWriter fw2 = new FileWriter("MyKeys/n_sk");
PemWriter writer2 = new PemWriter(fw2);
writer2.writeObject(new PemObject("PRIVATE KEY ", priv.getEncoded()));
writer2.close();
Security.addProvider(new BouncyCastleProvider());
Signature ecdsa;
ecdsa = Signature.getInstance("SHA256withECDSA"); // SHA512WITHECDSA SHA512withECDSA
ecdsa.initSign(getPrivate("MyKeys/n_sk"));
strByte = str.getBytes("UTF-8");
ecdsa.update(strByte);
realSig = ecdsa.sign();
sigEdata = Base64.getEncoder().encodeToString(realSig);
Thread.sleep(1000);
verify();
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
public static void verify() throws Exception {
verifySignature();
}
private static void verifySignature() throws Exception {
Signature sig = Signature.getInstance("SHA256withECDSA", "BC"); // SHA256withECDSA // SHA512withECDSA
// sig.initVerify(c.getPublicKey()); to verify using digi cert
sig.initVerify(getPublic("MyKeys/n.pem"));
sig.update(str.getBytes());
System.out.println(sig.verify(Base64.getDecoder().decode(sigEdata)));
// sig.verify(sigEdata.getBytes(Charset.defaultCharset()));
System.out.println(str);
}
private static PrivateKey getPrivate(String filename) throws Exception {
PemReader reader = new PemReader(new FileReader(filename));
PemObject pemObject = reader.readPemObject();
byte[] content = pemObject.getContent();
reader.close();
PKCS8EncodedKeySpec spec = new PKCS8EncodedKeySpec(content);
KeyFactory kf = KeyFactory.getInstance("EC");
return kf.generatePrivate(spec);
}
private static PublicKey getPublic(String filename) throws Exception {
PemReader reader = new PemReader(new FileReader(filename));
PemObject pemObject = reader.readPemObject();
byte[] content = pemObject.getContent();
reader.close();
X509EncodedKeySpec spec = new X509EncodedKeySpec(content);
KeyFactory kf = KeyFactory.getInstance("EC");
return kf.generatePublic(spec);
}
}

encryption and decryption using socket server and des algorithm

creating a server-client java App for encryption and Decryption using DES algorithm and a file to save my key in it ,socket for client server comunication
i have problem in the decrypt function
this is my server code
import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
import java.net.ServerSocket;
import java.net.Socket;
import java.util.Date;
import javax.crypto.*;
import java.security.*;
import java.util.Arrays;
import java.util.Base64;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.crypto.spec.SecretKeySpec;
/**
*
* #author ASUS
*/
public class Server {
public static void main(String[] args) throws IOException, NoSuchAlgorithmException, NoSuchPaddingException, InvalidKeyException, IllegalBlockSizeException, BadPaddingException {
try (ServerSocket listener = new ServerSocket(3001)) {
System.out.println("The date server is running...");
while (true) {
try (Socket socket = listener.accept()) {
Key k = Client.getkey("D://key.txt");
DataInputStream in = new DataInputStream(socket.getInputStream());
String x = in.readUTF();
System.out.println(k);
System.out.println(x);
System.out.println(Decrypt(x, k));
}
}
}
}
public static String Decrypt(String cipherText, Key k) throws NoSuchAlgorithmException, NoSuchPaddingException, InvalidKeyException, IllegalBlockSizeException, BadPaddingException, UnsupportedEncodingException {
Cipher cipher = Cipher.getInstance("DES/ECB/PKCS5Padding");
cipher.init(Cipher.DECRYPT_MODE, k);
return new String (cipher.doFinal(Base64.getDecoder().decode(cipherText)),"UTF-8");
}
public static void gen_key() throws NoSuchAlgorithmException {
KeyGenerator kg = KeyGenerator.getInstance("DES");
Key k = kg.generateKey();
String encodedKey = Base64.getEncoder().encodeToString(k.getEncoded());
try {
FileWriter myWriter = new FileWriter("D://key.txt");
myWriter.write(encodedKey);
myWriter.close();
System.out.println("Successfully wrote key to the file.");
} catch (IOException e) {
System.out.println("An error occurred.");
e.printStackTrace();
}
}
public static Key getkey(String filename) throws FileNotFoundException, IOException {
InputStream is = new FileInputStream(filename);
BufferedReader buffer = new BufferedReader(new InputStreamReader(is));
String line = buffer.readLine();
StringBuilder sb = new StringBuilder();
while (line != null) {
sb.append(line);
line = buffer.readLine();
}
String fileAsString = sb.toString();
byte[] decodedkey = Base64.getDecoder().decode(fileAsString);
SecretKey originkey = new SecretKeySpec(decodedkey, 0, decodedkey.length, "DES");
return originkey;
}
}
and this is client code
import java.io.BufferedReader;
import java.io.File;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.Scanner;
import java.net.Socket;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import javax.crypto.*;
import java.security.*;
import java.util.Arrays;
import java.util.Base64;
import javax.crypto.spec.SecretKeySpec;
/**
*
* #author ASUS
*/
public class Client {
public static void main(String[] args) throws IOException, NoSuchAlgorithmException, NoSuchPaddingException, InvalidKeyException, IllegalBlockSizeException, BadPaddingException {
gen_key();
byte[] r;
Key k=getkey("D://key.txt");
r = encrypt("fatimaalzahrasha",k);
Socket socket = new Socket("127.0.0.1", 3001);
DataOutputStream os=new DataOutputStream(socket.getOutputStream());
os.writeUTF(r.toString());
}
public static Key getkey(String filename) throws FileNotFoundException, IOException{
InputStream is=new FileInputStream(filename);
BufferedReader buffer=new BufferedReader(new InputStreamReader(is));
String line=buffer.readLine();
StringBuilder sb=new StringBuilder();
while(line!=null)
{sb.append(line);
line=buffer.readLine();}
String fileAsString=sb.toString();
byte[] decodedkey=Base64.getDecoder().decode(fileAsString);
SecretKey originkey=new SecretKeySpec(decodedkey, 0,decodedkey.length,"DES");
return originkey;}
public static void gen_key() throws NoSuchAlgorithmException{
KeyGenerator kg=KeyGenerator.getInstance("DES");
Key k=kg.generateKey();
String encodedKey=Base64.getEncoder().encodeToString(k.getEncoded());
try {
FileWriter myWriter = new FileWriter("D://key.txt");
myWriter.write(encodedKey);
myWriter.close();
System.out.println("Successfully wrote key to the file.");
} catch (IOException e) {
System.out.println("An error occurred.");
e.printStackTrace();
}
}
public static byte [] encrypt(String plain,Key k ) throws NoSuchAlgorithmException, NoSuchPaddingException, InvalidKeyException, IllegalBlockSizeException, BadPaddingException, UnsupportedEncodingException
{
Cipher cipher = Cipher.getInstance("DES");
cipher.init(Cipher.ENCRYPT_MODE, k);
byte[] data = plain.getBytes();
byte[] result = cipher.doFinal(data);
return result;
}
}
when i run server then client i have this output
The date server is running...
javax.crypto.spec.SecretKeySpec#fffe78c8
[B#1412c2f
Exception in thread "main" java.lang.IllegalArgumentException: Illegal base64 character 5b
at java.util.Base64$Decoder.decode0(Base64.java:714)
at java.util.Base64$Decoder.decode(Base64.java:526)
at Server.Decrypt(Server.java:60)
at Server.main(Server.java:48)
C:\Users\ASUS\AppData\Local\NetBeans\Cache\8.2\executor-snippets\run.xml:53: Java returned: 1
BUILD FAILED (total time: 11 seconds)

The error results of different formats of the encrypted text ("ciphertext"). On client side the output of the encrypt method is a byte array that get transferred via Socket to the server. On server side the input of the decryption method awaits a string in Base64-encoding.
So you can send the encrypted data as a byte array and leave out the decoding part OR you encode your byte array on client side with Base64 like
byte[] r;
r = encrypt("fatimaalzahrasha",k);
String rBase64 = Base64.getEncoder().encodeToString(r);
os.writeUTF(rBase64);

Signature Verification in JAVA and Signature Length

I developed a java application as follows such that it reads public key from PEM file and then verifies the signature. I received this signature from the outside (a company) and it has been generated using RSA2048. However I receive following error message:
"Signature length not correct: got 384 but was expecting 256."
Must I do some modification on this signature before verification?
package read_key_pck;
import static java.nio.charset.StandardCharsets.UTF_8;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.security.KeyFactory;
import java.security.NoSuchAlgorithmException;
import java.security.NoSuchProviderException;
import java.security.PrivateKey;
import java.security.PublicKey;
import java.security.Security;
import java.security.Signature;
import java.security.spec.InvalidKeySpecException;
import java.security.spec.PKCS8EncodedKeySpec;
import java.security.spec.X509EncodedKeySpec;
import java.util.Base64;
import org.bouncycastle.jce.provider.BouncyCastleProvider;
public class Main {
//protected final static Logger LOGGER = Logger.getLogger(Main.class);
public final static String RESOURCES_DIR = "C:\\Users\\KX5710\\eclipse-workspace\\read_key\\src\\read_key_pck\\";
public static boolean verify(String plainText, String signature, PublicKey publicKey) throws Exception {
Signature publicSignature = Signature.getInstance("SHA256withRSA");
publicSignature.initVerify(publicKey);
publicSignature.update(plainText.getBytes(UTF_8));
byte[] signatureBytes = Base64.getDecoder().decode(signature);
return publicSignature.verify(signatureBytes);
}
public static void main(String[] args) throws Exception {
Security.addProvider(new BouncyCastleProvider());
PublicKey pub = null;
KeyFactory factory = KeyFactory.getInstance("RSA", "BC");
try {
/*PrivateKey priv = generatePrivateKey(factory, RESOURCES_DIR
+ "id_rsa");*/
pub = generatePublicKey(factory, RESOURCES_DIR
+ "rsa_2048_pub.pem");
} catch (InvalidKeySpecException e) {
e.printStackTrace();
}
String encodedPublicKey = Base64.getEncoder().encodeToString(pub.getEncoded());
System.out.println("publickey: " + encodedPublicKey);
boolean isCorrect = verify(" 5 5.00 1.80", "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", pub);
System.out.println("Signature verification: " + isCorrect);
}
private static PublicKey generatePublicKey(KeyFactory factory,
String filename) throws InvalidKeySpecException,
FileNotFoundException, IOException {
PemFile pemFile = new PemFile(filename);
byte[] content = pemFile.getPemObject().getContent();
X509EncodedKeySpec pubKeySpec = new X509EncodedKeySpec(content);
return factory.generatePublic(pubKeySpec);
}
}
package read_key_pck;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import org.bouncycastle.util.io.pem.PemObject;
import org.bouncycastle.util.io.pem.PemReader;
public class PemFile {
private PemObject pemObject;
public PemFile(String filename) throws FileNotFoundException, IOException {
PemReader pemReader = new PemReader(new InputStreamReader(
new FileInputStream(filename)));
try {
this.pemObject = pemReader.readPemObject();
} finally {
pemReader.close();
}
}
public PemObject getPemObject() {
return pemObject;
}
}

Your signature is encoded as HEX not as BASE64.
Change
byte[] signatureBytes = Base64.getDecoder().decode(signature);
with
byte[] signatureBytes = DatatypeConverter.parseHexBinary(signature)

Java RSA encrypted AES key

I have an RSA private key that I am trying to decrypt another files contents that has an AES key in it. So far all I can seem to get to return from the processes is jargon. Not really sure what I am doing wrong in the below code. I have looked on google and have seen this done at least a 100 different ways.
import java.io.*;
import java.io.IOException;
import java.security.KeyFactory;
import java.security.interfaces.RSAPrivateKey;
import java.security.GeneralSecurityException;
import java.security.spec.PKCS8EncodedKeySpec;
import javax.crypto.Cipher;
import javax.crypto.CipherInputStream;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.FileUtils;
public class RsaEncryption {
private Cipher _pkCipher;
public RsaEncryption() throws GeneralSecurityException {
// create RSA public key cipher
_pkCipher = Cipher.getInstance("RSA");
}
public String loadKey(File in, String privateKey) throws GeneralSecurityException, IOException, Exception {
privateKey = privateKey.replaceAll("-+.*?-+", "");
byte[] encodedKey = Base64.decodeBase64(privateKey);
// create private key
PKCS8EncodedKeySpec privateKeySpec = new PKCS8EncodedKeySpec(encodedKey);
KeyFactory kf = KeyFactory.getInstance("RSA");
RSAPrivateKey pk = (RSAPrivateKey) kf.generatePrivate(privateKeySpec);
// read AES key
_pkCipher.init(Cipher.DECRYPT_MODE, pk);
byte[] encryptedBytes = FileUtils.readFileToByteArray(in);
ByteArrayInputStream fileIn = new ByteArrayInputStream(encryptedBytes);
CipherInputStream cis = new CipherInputStream(fileIn, _pkCipher);
DataInputStream dis = new DataInputStream(cis);
byte[] decryptedData = new byte[32];
dis.read(decryptedData);
String key = new String(decryptedData);
return key;
}
}
UPDATE
New way with bouncy castles pem converter still not working
import java.io.StringReader;
import java.io.File;
import java.io.IOException;
import java.security.KeyPair;
import java.security.interfaces.RSAPrivateKey;
import java.security.GeneralSecurityException;
import java.security.interfaces.RSAPublicKey;
import javax.crypto.Cipher;
import org.apache.commons.io.FileUtils;
import org.bouncycastle.openssl.PEMKeyPair;
import org.bouncycastle.openssl.PEMParser;
import org.bouncycastle.openssl.jcajce.JcaPEMKeyConverter;
public class RsaEncryption {
private Cipher _pkCipher;
private RSAPrivateKey _PrivateKey;
private RSAPublicKey _PublicKey;
public RsaEncryption(String privateKey) throws GeneralSecurityException, IOException {
loadKey(privateKey);
// create RSA public key cipher
_pkCipher = Cipher.getInstance("RSA/None/PKCS1Padding", "BC");
}
private void loadKey(String privateKey) throws IOException {
PEMParser pemParser = new PEMParser(new StringReader(privateKey));
PEMKeyPair pemKeyPair = (PEMKeyPair) pemParser.readObject();
JcaPEMKeyConverter converter = new JcaPEMKeyConverter().setProvider("BC");
KeyPair keyPair = converter.getKeyPair(pemKeyPair);
_PrivateKey = (RSAPrivateKey) keyPair.getPrivate();
_PublicKey = (RSAPublicKey) keyPair.getPublic();
pemParser.close();
}
public String decrypt(File in) throws GeneralSecurityException , IOException{
_pkCipher.init(Cipher.DECRYPT_MODE, _PrivateKey);
byte[] encryptedBytes = FileUtils.readFileToByteArray(in);
String key = new String(_pkCipher.doFinal(encryptedBytes));
System.out.println(key);
return key;
}
public RSAPrivateKey getPrivateKey() { return _PrivateKey; }
public RSAPublicKey getPublicKey() { return _PublicKey; }
}

RSA can only encrypt a small amount of data which must be processed as a chunk. You don't need a stream for that. Simply call
byte[] aesKey = _pkCipher.doFinal(FileUtils.readFileToByteArray(in));
to get the AES key.

JCE jars where in the wrong directory worked just fine once they got put in the correct directory.

RSA encryption(java) read the string input

I do RSA encryption and having a problem. I want to encrypt a string.To convert the string, I already have the rsHex array to convert it.. I run the source code but it give me error say "the system cannot find the file specified" Here is my source code. How do I solve his? Thanks for helping me :)
import de.flexiprovider.api.keys.PrivateKey;
import de.flexiprovider.api.keys.PublicKey;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.math.BigInteger;
import java.security.InvalidKeyException;
import java.security.Key;
import java.security.KeyFactory;
import java.security.KeyPair;
import java.security.KeyPairGenerator;
import java.security.NoSuchAlgorithmException;
import java.security.spec.InvalidKeySpecException;
import java.security.spec.RSAPrivateKeySpec;
import java.security.spec.RSAPublicKeySpec;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.crypto.BadPaddingException;
import javax.crypto.Cipher;
import javax.crypto.IllegalBlockSizeException;
import javax.crypto.NoSuchPaddingException;
public class RSA {
private String str, s;
private String chipertext;
private byte[] cipherData;
public RSA(String string) throws Exception {
try {
String input = string;
FileReader read = new FileReader(input);
BufferedReader reader = new BufferedReader(read);
while ((s = reader.readLine()) != null) {
byte[] theByteArray = s.getBytes();
setUserinput(string);
rsHex(theByteArray);
}
} catch (Exception ex) {
Logger.getLogger(RSA.class.getName()).log(Level.SEVERE, null, ex);
}
//Creating an RSA key pair in Java
KeyPairGenerator kpg = KeyPairGenerator.getInstance("RSA"); //instance of KeyPairGenerator
kpg.initialize(1024);//bit length of the modulus that required
KeyPair kp = kpg.genKeyPair();//returns a KeyPair object
Key publicKey = kp.getPublic(); //pull out the public and private keys
Key privateKey = kp.getPrivate();
//Saving the public and private key
//private key will be placed on our server, and the public key distributed to clients.
KeyFactory fact = KeyFactory.getInstance("RSA");
RSAPublicKeySpec pub = (RSAPublicKeySpec) fact.getKeySpec(publicKey, RSAPublicKeySpec.class);
RSAPrivateKeySpec priv = (RSAPrivateKeySpec) fact.getKeySpec(privateKey, RSAPrivateKeySpec.class);
// Save the file to local drive
saveToFile("c:\\public.key", pub.getModulus(), pub.getPublicExponent());
saveToFile("c:\\private.key", priv.getModulus(),priv.getPrivateExponent());
}
private void rsHex(byte[] bytes) throws Exception {
StringBuilder hex = new StringBuilder();
for (byte b : bytes) {
String hexString = Integer.toHexString(0x00FF & b);
hex.append(hexString.length() == 1 ? "0" + hexString : hexString);
}
setChipertext(hex.toString());
}
//save the moduli and exponents to file, we can just use boring old serialisation
public void saveToFile(String fileName, BigInteger mod, BigInteger exp) throws IOException {
FileOutputStream f = new FileOutputStream(fileName);
ObjectOutputStream oos = new ObjectOutputStream(f);
oos.writeObject(mod);
oos.writeObject(exp);
oos.close();
}
////Encryption
//initialise the cipher with the public key that we previously saved to file.
PublicKey readKeyFromFile(String keyFileName) throws IOException {
PublicKey key = null;
try {
FileInputStream fin = new FileInputStream(keyFileName);
ObjectInputStream ois = new ObjectInputStream(fin);
BigInteger m = (BigInteger) ois.readObject();
BigInteger e = (BigInteger) ois.readObject();
RSAPrivateKeySpec keySpec = new RSAPrivateKeySpec(m, e);
KeyFactory fact = KeyFactory.getInstance("RSA");
java.security.PublicKey pubKey = fact.generatePublic(keySpec);
ois.close();
}
catch (Exception e) {
e.printStackTrace();
}
return key;
}
public void rsaEncrypt(String str)throws Exception {
PublicKey pubKey = readKeyFromFile(str);
Cipher cipher = Cipher.getInstance("RSA");
cipher.init(Cipher.ENCRYPT_MODE, pubKey);//initialise the cipher
cipherData = cipher.doFinal(str.getBytes());//passing in the data to be encrypted
rsHex(cipherData);
}
public String getUserinput() {
return str;
}
public String getChipertext() {
return chipertext;
}
public void setUserinput(String input) {
this.str = input;
}
public void setChipertext(String chipertext) throws Exception {
this.chipertext = chipertext;
}
}
----main Program------
import java.util.Scanner;
public class TWO{
public static void main(String[] args) throws Exception{
Scanner scan = new Scanner(System.in);
System.out.println("Insert your string");
String str = scan.nextLine();
RSA two = new RSA(str);
System.out.println("Encrypted: "+ two.getChipertext());
}
}

The problem is that you're taking an input string from the user, but then your code is treating this as though it was a filename by constructing a FileReader with that string.
Instead of all that nonsense with the FileReader and BufferedReader, is there any reason why you don't just use string.getBytes()?
You also seem to be making life awfully complicated for yourself: you're taking a string, converting into a byte array, then converting that into a string again (with hex representation), then converting that into a byte array again. That's an awful lot of messing about when you could really just take the byte representation of the original string (as given to you by getBytes()) and pass that directly to the RSA encryption.